Novel antimicrobial peptides

ABSTRACT

This invention provides novel antimicrobial peptides that are effective to inhibit growth and/or proliferation of various gram positive bacteria. In particular, the peptides are effective against  Streptococcus mutans  a common oral pathogen and the causative agent of dental caries.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of and priority to U.S. Ser. No.60/880,783, filed on Jan. 16, 2007, which is incorporated herein byreference in its entirety for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

This work was supported in part by Grant No: MD01831 from the NationalInstitutes of Health. The government of the United States of America hascertain rights in this work.

FIELD OF THE INVENTION

This invention pertains to the field of antimicrobial compounds. Inparticular, this invention pertains to the identification of novelantimicrobial peptides effective against Streptococcus mutans and otherbacteria.

BACKGROUND OF THE INVENTION

Antimicrobial peptides (AMPs) have recently come to the forefront aspotential antibiotic surrogates due to their robust killing activityagainst a wide-spectrum of bacterial species including drug-resistantstrains. AMPs are genetically common molecules of innate immunity thathave been discovered in single-cell and multicellular forms of life(Tossi et al. (2000) Biopolymers 55: 4-30; Diamond (2001) Biologist(London) 48: 209-212; Lehrer and Ganz (2002) Curr. Opin. Immunol. 14:96-102; Brogden et al. (2003) Int. J. Antimicrob. Agents 22: 465-478).Although they can differ dramatically by peptide sequence andpost-translational modification (linear, circular, etc), the majority ofAMPs appear to kill bacteria by the disruption of lipid membranes,though the details of this mechanism appear to vary widely (Shai (2002)Biopolymers 66: 236-248; Brogden (2005) Nat. Rev. Microbiol. 3:238-250). Previous observations have indicated the critical role ofgeneral hydrophobic and cationic character in AMP function, includingthe significant contribution of aromatic Trp and cationic Arg residuesfound in many AMPs (Chan et al. (2007) Biochim Biophys Acta. 51(4):1351-1359; Wei et al. (2006) J. Bacteriol. 188: 328-334). Despite theirsmall size (most AMPs are under 50 amino acids), secondary structurealso appears to play an important role in activity. Certain linear AMPscan adopt an α-helical or (3-strand confirmation upon interaction withhydrophobic environments (such as detergents or lipid vesicles) thatmimic bacterial membranes, suggesting these conformational changes arenecessary for antimicrobial function (Kiyota et al. (1996) Biochemistry35: 13196-13204; Wei et al. (2006) J. Bacteriol. 188: 328-334; Wimmer etal. (2006) Biochemistry 45: 481-497). Additionally, the formation of amembrane-active a-helix (and other structures) appears to require anamphipathic spatial arrangement of residues, i.e., a gradient ofhydrophobicity across the surface of the peptide (Kiyota et al. (1996)Biochemistry 35: 13196-13204; Shai (1999) Biochim Biophys Acta 1462:55-70; Lee (2002) Curr Pharm Des 8: 795-813).

Previously, rational design of antimicrobial peptides has focused mainlyon varying existing natural sequences, or developing novel peptides fromlarge combinatorial libraries (Kiyota et al. (1996) Biochemistry 35:13196-13204; Blondelle and Lohner (2000) Biopolymers 55: 74-87; Hong etal. (2001) Peptides 22: 1669-1674; Sawai et al. (2002) Protein Eng. 15:225-232). These efforts have yielded valuable information on AMPstructure-activity.

Streptococcus mutans, a common oral pathogen and the causative agent ofdental caries, has persisted and even thrived on the tooth surfacedespite constant efforts to remove or eradicate them. New therapeuticsagainst this organism are sorely needed, as S. mutans is a persistentcolonizer of the tooth surface in the presence of dietary sugars and canremain in the oral microflora (known as dental plaque) despite dedicatedmechanical removal (tooth brushing) and general antiseptic efforts(Keene and Shklair (1974) J. Dent. Res. 53: 1295).

SUMMARY OF THE INVENTION

This invention pertains to the discovery of novel antimicrobialpeptides. In certain embodiments the peptides show significant activityagainst Gram positive bacteria, particularly against Gram positivebacteria of the oral cavity (e.g., Streptococcus mutans). The peptidesare effective in the formulation of various antimicrobial compositionsand/or in the prevention or reduction of the incidence of dental caries.

Accordingly, in certain embodiments, this invention provides anantimicrobial peptide the peptide comprising the following amino acidmotif or a circular permutation of the following amino acid motif:(H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵)_(n), where n ranges from 1 to 5 and can incrementby units of 0.1; H¹, H², H³, H⁴, and H⁵ are independently selectedhydrophobic or hydrophilic amino acids; C¹, C², C³, C⁴, and C⁵ areindependently selected uncharged amino acids, positively charged aminoacids, or negatively charged amino acids; the peptide forms an alphahelix; and the peptide is effective to kill or inhibit the growth and/orproliferation of Streptococcus mutans in culture. In certain embodimentsC¹, C², C³, C⁴, and C⁵ are independently selected positively chargedamino acids, or negatively charged amino acids. In certain embodimentsthe uncharged amino acids are independently selected from the groupconsisting of S, T, and Y (or analogues, derivatives, or conservativesubstitutions thereof), and/or the positively charged amino acids areindependently selected from the group consisting of K, R, and H (oranalogues, derivatives, or conservative substitutions thereof), and/orthe negatively charged amino acids are independently selected from thegroup consisting of N, Q, D, and E (or analogues, derivatives, orconservative substitutions thereof), and/or the hydrophobic orhydrophilic amino acids are independently selected from the groupconsisting of using L, I, V, W, and F (or analogues, derivatives, orconservative substitutions thereof). In certain embodiments the peptidehas at least a +3 net positive charge at physiological pH. In certainembodiments, n is 1.1; and the peptide comprises the motifH¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶, where H⁶ is an independently selectedhydrophobic amino acid. Illustrative n=1.1 peptides include, but are notlimited to FKKFWKWFRRF (SEQ ID NO:31) (B-33), LKRFLKWFKRF (SEQ ID NO:32)(B-34), KLFKRWKHLFR (SEQ ID NO:33) (B-35), RLLKRFKHLFK (SEQ ID NO:34)(B-36), FKTFLKWLHRF (SEQ ID NO:35) (B-37), IKQLLHFFQRF (SEQ ID NO:36)(B-38), KLLQTFKQIFR (SEQ ID NO:37) (B-39), RILKELKNLFK (SEQ ID NO:38)(B-40), LKQFVHFIHRF (SEQ ID NO:39) (B-41), VKTLLHIFQRF (SEQ ID NO:40)(B-42), KLVEQLKEIFR (SEQ ID NO:41) (B-43), RVLQELKQILK (SEQ ID NO:42)(B-44), VKNLAELVHRF (SEQ ID NO:43) (B-45), ATHLLHALQRF (SEQ ID NO:44)(B-46), KLAENVKEILR (SEQ ID NO:45) (B-47), RALHEAKEALK (SEQ ID NO:46)(B-48), FHYFWHWFHRF (SEQ ID NO:47) (B-49), LYHFLHWFQRF (SEQ ID NO:48)(B-50), YLFQTWQHLFR (SEQ ID NO:49) (B-51), YLLTEFQHLFK (SEQ ID NO:50)(B-52), FKTFLQWLHRF (SEQ ID NO:51) (B-53), IKTLLHFFQRF (SEQ ID NO:52)(B-54), KLLQTFNQIFR (SEQ ID NO:53) (B-55), TILQSLKNIFK (SEQ ID NO:54)(B-56), LKQFVKFIHRF (SEQ ID NO:55) (B-57), VKQLLKIFNRF (SEQ ID NO:56)(B-58), KLVQQLKNIFR (SEQ ID NO:57) (B-59), RVLNQVKQILK (SEQ ID NO:58)(B-60), VKKLAKLVRRF (SEQ ID NO:59) (B-61), AKRLLKVLKRF (SEQ ID NO:60)(B-62), KLAQKVKRVLR (SEQ ID NO:61) (B-63), and RALKRIKHVLK (SEQ IDNO:62) (B-64). In certain embodiments n is 1.4; and the peptidecomprises the motif H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶C⁶C⁷H⁷, where H⁶, and H⁷ areindependently selected hydrophobic amino acids, and C⁶ and C⁷ areindependently selected positively or negatively charged amino acids.Illustrative n=1.4 peptides include, but are not limited toKLKKLLKKLKKLLK (SEQ ID NO:64) (α-5), LKLLKKLLKLLKKF (SEQ ID NO:65)(α-6), LQLLKQLLKLLKQF (SEQ ID NO:66) (α-7), RWRRWWRHFHHFFH (SEQ IDNO:68) (α-9), KLKKLLKRWRRWWR (SEQ ID NO:69) (α-10), RWRRLLKKLHHLLH (SEQID NO:70) (α-11), and KLKKLLKHLHHLLH (SEQ ID NO:71) (α-12).

In certain embodiments the antimicrobial peptide (AMP) is a peptidecomprising seven contiguous amino acids where all but two amino acidsare Arg or Trp, or derivatives or analogues thereof; the two non-Arg orTrp amino acids are Lys or Phe, or derivatives or analogues thereof; andthe N-terminal residue is Arg or a derivative or analogue thereof. Invarious embodiments all but two of the amino acids are Arg or Trp (orderivatives or analogues thereof); the two non-Arg or Trp amino acidsare Lys or Phe (or derivatives or analogues thereof); and the N-terminalresidue is Arg (or a derivative or analogue thereof). In certainembodiments the peptide comprises an amino acid sequence selected fromthe group consisting of RRRRWWW (SEQ ID NO:72) (1C-1), RRWWRRW (SEQ IDNO:73) (1C-2), RRRWWWR (SEQ ID NO:74) (1C-3), RWRWRWR (SEQ ID NO:75)(1C-4), RRRFWWR (SEQ ID NO:76) (2C-1), RRWWRRF (SEQ ID NO:77) (2C-2),RRRWWWF (SEQ ID NO:78) (2C-3), RWRWRWF (SEQ ID NO:79) (2C-4), RRRRWWK(SEQ ID NO:80) (3C-1), RRWWRRK (SEQ ID NO:81) (3C-2), RRRWWWK (SEQ IDNO:82) (3C-3), RWRWRWK (SEQ ID NO:83) (3C-4), RRRKWWK (SEQ ID NO:84)(4C-1), RRWWRRK (SEQ ID NO:85) (4C-2), RRRKWWK (SEQ ID NO:86) (4C-3),and RWRWRWK (SEQ ID NO:87) (4C-4).

Also provided are acid-activated antimicrobial peptides (AMPs)comprising an amphipathic helical peptide ranging in length from about 7to about 11 amino acids where the majority (more than half) of chargedresidues are His or a derivative or analogue thereof that caries acationic charge at an acidic pH, where the peptide has substantially noantimicrobial activity at neutral pH, but has antimicrobial activityagainst S. mutans at an acidic pH. In certain embodiments all thecharged residues are His or a derivative or analogue thereof that cariesa cationic charge at an acidic pH (e.g., pH 6 or lower). In certainembodiments the peptide comprises alternating repeats of HH and FF. Incertain embodiments the peptide comprises the amino acid sequence KLLK(SEQ ID NO:166) at one or both termini. In certain embodiments KLLK (SEQID NO:166) at one or both termini where the KLLK is joined to theterminus by a linker (e.g., GAT, SEQ ID NO:167). In certain embodimentsthe peptide comprises the amino acid sequence FHFFHHFFHFFHHF (SEQ IDNO:168). Illustrative acid-activated AMPs include, but are not limitedto HHFFHHFHHFFHHF (SEQ ID NO:109) (AA-1), FHFFHHFFHFFHHF (SEQ ID NO:110)(AA-2), KLLKGATFHFFHHFFHFFHHF (SEQ ID NO:111) (AA-3), KLLKFHFFHHFFHFFHHF(SEQ ID NO:112) (AA-4), FHFFHHFFHFFHHFKLLK (SEQ ID NO:113) (AA-5),FHYFWHWFHRF (SEQ ID NO:114) (AA-6), and LYHFLHWFQRF (SEQ ID NO:115)(AA-7).

In certain embodiments, this invention provides killing library #7 AMPs.Such peptides include LKQKLKILF (SEQ ID NO:116 (S6L1-2), LKQLKAGIY (SEQID NO:117) (S6L1-3), VGKCVKLLY (SEQ ID NO:118) (S6L1-4), KFVKLI LAY (SEQID NO:119) (S6L1-5), KLVKLVFLY (SEQ ID NO:120) (S6L1-6), IKVFAKQKY (SEQID NO:121) (S6L1-7), and RFRHFQERY (SEQ ID NO:122) (S6L1-8).

In certain embodiments, this invention provides beta-deletion libraryAMPs. Such peptides include FVFRHKWVWKHRFLF (SEQ ID NO:123) (S3L8-1),VFI VWVHKHVLF (SEQ ID NO:124) (S3L8-2), WRWRARWRWRLRWRF (SEQ ID NO:125)(S3L8-3), WR1HLRARLHVKFRF (SEQ ID NO:126) (S3L8-4), LRIHARFKVHIRLKF (SEQID NO:127) (S3L8-5), FHIKFRVHLKVRFHF (SEQ ID NO:128) (S3L8-6),FHVK1HFRLHVKFHF (SEQ ID NO:129) (S3L8-7), LHIHAHFHVHIHLHF (SEQ IDNO:130) (S3L8-8), FKIHFRLKVHIRFKF (SEQ ID NO:131) (S3L8-9),FKAHIRFKLRVKFHF (SEQ ID NO:132) (S3L8-10), LKAKIKFKVKLKIKF (SEQ IDNO:133) (S3L8-11), WIWKHKFLHRHFLF (SEQ ID NO:134) (S3L8-12),VFLHRHVIKHKLVF (SEQ ID NO:135) (S3L8-13), FLHKHVLRHRIVF (SEQ ID NO:136)(S3L8-14), VFKHKIVHRHILF (SEQ ID NO:137) (S3L8-15), FLFKHLFLHRIFF (SEQID NO:138) (S3L8-16), LFKHILIHRVIF (SEQ ID NO:139) (S3L8-17),FLHKHLFKHKLF (SEQ ID NO:140) (S3L8-18), VFRHRFIHRHVF (SEQ ID NO:141)(S3L8-19), FIHKLVHKHVLF (SEQ ID NO:142) (S3L8-20), VLRHLFRHRIVF (SEQ IDNO:143) (S3L8-21), LVHKLILRHLLF (SEQ ID NO:144) (S3L8-22), VFKRVLI HKLIF(SEQ ID NO:145) (S3L8-23), IVRKFLFRHKVF (SEQ ID NO:146) (S3L8-24),VLKHVIAHKRLF (SEQ ID NO:147) (S3L8-25), FIRKFLFKHLF (SEQ ID NO:148)(S3L8-26), VIRHVWVRKLF (SEQ ID NO:149) (S3L8-27), FLFRHRFRHRLVF (SEQ IDNO:150) (S3L8-28), LFLHKHAKHKFLF (SEQ ID NO:151) (S3L8-29), FKHKFKHKFIF(SEQ ID NO:152) (S3L8-30), LRHRLRHRLIF (SEQ ID NO:153) (S3L8-31),LILKFLFKFVF (SEQ ID NO:154) (S3L8-32), VLIRILVRVIF (SEQ ID NO:155)(S3L8-33), FRHRFRHRF (SEQ ID NO:156) (S3L8-34), LKHKLKHKF (SEQ IDNO:157) (S3L8-35), FKFKHKLIF (SEQ ID NO:158) (S3L8-36), LRLRHRVLF (SEQID NO:159) (S3L8-37), FKFLFKFLF (SEQ ID NO:160) (S3L8-38), LRLFLRWLF(SEQ ID NO:161) (S3L8-39), FKFLFKHKF (SEQ ID NO:162) (S3L8-40),LRLFLRHRF (SEQ ID NO:163) (S3L8-41), FKFLFKF (SEQ ID NO:164) (S3L8-42),and LRLFLRF (SEQ ID NO:165) (S3L8-43).

In certain embodiments the any of the peptides described herein areattached to a second antimicrobial peptide (AMP) thereby forming acompound antimicrobial peptide. The two peptides can be chemicallyconjugated directly or through a linker, or expressed (or synthesized)as a fusion protein with or without a peptide linker. In certainembodiments the second antimicrobial peptide is: a peptide comprisingthe following amino acid motif or a circular permutation of thefollowing amino acid motif: (H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵)_(n) where n rangesfrom 1 to 5 and can increment by units of 0.1; H¹, H², H³, H⁴, and H⁵are independently selected hydrophobic or hydrophilic amino acids; andC¹, C², C³, C⁴, and C⁵ are independently selected neutral amino acids,positively charged amino acids, or negatively charged amino acids; orthe peptide comprising the seven contiguous amino acids where all buttwo amino acids are Arg or Trp, or derivatives or analogues thereof; thetwo non-Arg or Trp amino acids are Lys or Phe, or derivatives oranalogues thereof; and the N-terminal residue is Arg or a derivative oranalogue thereof. In certain embodiments the second antimicrobacterialpeptide is a peptide listed in Table 6, Table 10, Table 11, or Table 12.

In certain embodiments the any of the peptides or compound AMPsdescribed herein further comprise a free amine at the carboxyl terminus(e.g., provided by arginine or lysine, or by an amidated non-cationicresidue). In certain embodiments any of the peptides or compound AMPsdescribed herein are pegylated. In certain embodiments any of thepeptides described herein or compound AMPs bear one or more protectinggroups (e.g., acetyl, amide, and 3 to 20 carbon alkyl groups, Fmoc,Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group,9-florenecarboxylic group, 9-fluorenone-1-carboxylic group,benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt),4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr),Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl(Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pmc), 4-methylbenzyl(MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl),Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys),1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl(2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z),2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom),t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum),t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA),and the like). In certain embodiments the any of the peptides describedherein or compound AMPs comprise all naturally occurring amino acids. Incertain embodiments the any of the peptides described herein compriseone or more “D” amino acids and/or one or more beta amino acids. Incertain embodiments any of the peptides described herein or compoundAMPs are labeled with a detectable label (e.g., an enzymatic label, afluorescent label, a colorimetric label, a spin label, a radioactivelabel, and the like).

Also provided are pharmaceutical formulations comprising an any one ormore of the antimicrobial peptides or compound AMPs described herein anda pharmaceutically acceptable excipient. In certain embodiments theformulation is a unit dosage formulation. In certain embodiments theexcipient is acceptable for administration to an oral mucosa.

In certain embodiments this invention provides a health care product,e.g., a prescription or over the counter product for use in a home, fortravel, at work, in a dental office, at a hospital, etc., comprising anyone or more of the antimicrobial peptides or compound AMPs describedherein where the antimicrobial peptide(s) and/or compound AMPs arecontained in a product selected from the group consisting of toothpaste,mouthwash, a tooth whitening strip or solution, s contact lens storage,wetting, or cleaning solution, dental floss, a toothpick, a toothbrushbristle, an oral sprays, an oral lozenge, a nasal spray, an aerosolizerfor oral and/or nasal application, and a wound dressing.

Also provided are methods of inhibiting the growth and/or proliferationof a bacterium (or other pathogen). The methods typically involvecontacting the bacterium or other pathogen with one or more of theantimicrobial peptides and/or compound AMPs described herein, in anamount sufficient to inhibit growth and/or proliferation of thebacterium or other pathogen. In certain embodiments the amount is anamount sufficient to kill the bacterium. In certain embodiments thebacterium is a Gram positive bacterium. In certain embodiments thebacterium is a Gram positive oral bacterium (e.g., Streptococcus sp.).In certain embodiments the contacting comprises contacting a mucosalsurface (e.g., an oral mucosa, a nasal mucosa, etc.).

Methods are also provided for inhibiting the formation of dental caries.The methods typically comprise contacting teeth and or oral mucosa withone or more of the antimicrobial peptides and/or compound AMPs describedherein in an amount sufficient to inhibit growth and/or proliferation ofS. mutans. In certain embodiments the contacting comprises contactingthe teeth and/or oral mucosa with a composition selected from the groupconsisting of a toothpaste, a mouthwash, a whitening strip or solution,a lozenge, an aerosol, and a swab.

In certain embodiments the peptides of this invention and/or the genericformulas herein expressly exclude the peptide B-33 (FKKFWKW FRRF, SEQ IDNO:31).

DEFINITIONS

The term “peptide” as used herein refers to a polymer of amino acidresidues typically ranging in length from 2 to about 50 residues. Incertain embodiments the peptide ranges in length from about 2, 3, 4, 5,7, 9, 10, or 11 residues to about 50, 45, 40, 45, 30, 25, 20, or 15residues. In certain embodiments the peptide ranges in length from about8, 9, 10, 11, or 12 residues to about 15, 20 or 25 residues. In certainembodiments the amino acid residues comprising the peptide are “L-form”amino acid residues, however, it is recognized that in variousembodiments, “D” amino acids can be incorporated into the peptide.Peptides also include amino acid polymers in which one or more aminoacid residues is an artificial chemical analogue of a correspondingnaturally occurring amino acid, as well as to naturally occurring aminoacid polymers. In addition, the term applies to amino acids joined by apeptide linkage or by other, “modified linkages” (e.g., where thepeptide bond is replaced by an α-ester, a β-ester, a thioamide,phosphonamide, carbomate, hydroxylate, and the like (see, e.g., Spatola,(1983) Chem. Biochem. Amino Acids and Proteins 7: 267-357), where theamide is replaced with a saturated amine (see, e.g., Skiles et al., U.S.Pat. No. 4,496,542, which is incorporated herein by reference, andKaltenbronn et al., (1990) Pp. 969-970 in Proc. 11th American PeptideSymposium, ESCOM Science Publishers, The Netherlands, and the like)).

The term “residue” as used herein refers to natural, synthetic, ormodified amino acids. Various amino acid analogues include, but are notlimited to 2-aminoadipic acid, 3-aminoadipic acid, beta-alanine(beta-aminopropionic acid), 2-aminobutyric acid, 4-aminobutyric acid,piperidinic acid, 6-aminocaproic acid, 2-aminoheptanoic acid,2-aminoisobutyric acid, 3-aminoisobutyric acid, 2-aminopimelic acid, 2,4diaminobutyric acid, desmosine, 2,2′-diaminopimelic acid,2,3-diaminopropionic acid, n-ethylglycine, n-ethylasparagine,hydroxylysine, allo-hydroxylysine, 3-hydroxyproline, 4-hydroxyproline,isodesmosine, allo-isoleucine, n-methylglycine, sarcosine,n-methylisoleucine, 6-n-methyllysine, n-methylvaline, norvaline,norleucine, ornithine, and the like. These modified amino acids areillustrative and not intended to be limiting.

“β-peptides” comprise of “β amino acids”, which have their amino groupbonded to the β carbon rather than the α-carbon as in the 20 standardbiological amino acids. The only commonly naturally occurring β aminoacid is β-alanine.

Peptoids, or N-substituted glycines, are a specific subclass ofpeptidomimetics. They are closely related to their natural peptidecounterparts, but differ chemically in that their side chains areappended to nitrogen atoms along the molecule's backbone, rather than tothe α-carbons (as they are in natural amino acids).

The terms “conventional” and “natural” as applied to peptides hereinrefer to peptides, constructed only from the naturally-occurring aminoacids: Ala, Cys, Asp, Glu, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn,Pro, Gln, Arg, Ser, Thr, Val, Trp, and Tyr. A compound of the invention“corresponds” to a natural peptide if it elicits a biological activity(e.g., antimicrobial activity) related to the biological activity and/orspecificity of the naturally occurring peptide. The elicited activitymay be the same as, greater than or less than that of the naturalpeptide. In general, such a peptoid will have an essentiallycorresponding monomer sequence, where a natural amino acid is replacedby an N-substituted glycine derivative, if the N-substituted glycinederivative resembles the original amino acid in hydrophilicity,hydrophobicity, polarity, etc. Thus, for example, the following pairs ofpeptides would be considered “corresponding”:

Ia. (SEQ ID NO: 1) Asp-Arg-Val-Tyr-Ile-His-Pro-Phe (Angiotensin II) andIb. (SEQ ID NO: 2) Asp-Arg-Val*-Tyr-Ile*-His-Pro-Phe; IIa.(SEQ ID NO: 3) Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg (Bradykinin) and IIb:(SEQ ID NO: 4) Arg-Pro-Pro-Gly-Phe*-Ser*-Pro-Phe*-Arg; IIIa:(SEQ ID NO: 5) Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr (β-Endorphin); and IIIb: (SEQ ID NO: 6)Gly-Gly-Phe*-Met-Ser*-Ser-Glu-Lys*-Ser-Gln-Ser*- Pro-Leu-Val*-Thr .In these examples, “Val*” refers to N-(prop-2-yl)glycine, “Phe*” refersto N-benzylglycine, “Ser*” refers to N-(2-hydroxyethyl)glycine, “Leu*”refers to N-(2-methylprop-1-yl)glycine, and “Ile*” refers toN-(1-methylprop-1-yl)glycine. The correspondence need not be exact: forexample, N-(2-hydroxyethyl)glycine may substitute for Ser, Thr, Cys, andMet;. N-(2-methylprop-1-yl)glycine may substitute for Val, Leu, and Ile.Note in IIIa and IIIb above that Ser* is used to substitute for Thr andSer, despite the structural differences: the sidechain in Ser* is onemethylene group longer than that of Ser, and differs from Thr in thesite of hydroxy-substitution. In general, one may use anN-hydroxyalkyl-substituted glycine to substitute for any polar aminoacid, an N-benzyl- or N-aralkyl-substituted glycine to replace anyaromatic amino acid (e.g., Phe, Trp, etc.), an N-alkyl-substitutedglycine such as N-butylglycine to replace any nonpolar amino acid (e.g.,Leu, Val, Ile, etc.), and an N-(aminoalkyl)glycine derivative to replaceany basic polar amino acid (e.g., Lys and Arg).

A “compound antimicrobial peptide” or “compound AMP” refers to aconstruct comprising two or more AMPs joined together. The AMPs can bejoined directly or through a linker. They can be chemically conjugatedor, where joined directly together or through a peptide linker cancomprise a fusion protein.

In certain embodiments, conservative substitutions of the amino acidscomprising any of the sequences described herein are contemplated. Invarious embodiments one, two, three, four, or five different residuesare substituted. The term “conservative substitution” is used to reflectamino acid substitutions that do not substantially alter the activity(e.g., antimicrobial activity and/or specificity) of the molecule.Typically conservative amino acid substitutions involve substitution oneamino acid for another amino acid with similar chemical properties (e.g.charge or hydrophobicity). The following six groups each contain aminoacids that are typical conservative substitutions for one another: 1)Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamicacid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K),Histidine (H); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine(V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

In certain embodiments, antimicrobial peptides compromising at least80%, preferably at least 85% or 90%, and more preferably at least 95% or98% sequence identity with any of the sequences described herein arealso contemplated. The terms “identical” or percent “identity,” refer totwo or more sequences that are the same or have a specified percentageof amino acid residues that are the same, when compared and aligned formaximum correspondence, as measured using one of the following sequencecomparison algorithms or by visual inspection. With respect to thepeptides of this invention sequence identity is determined over the fulllength of the peptide. For sequence comparison, typically one sequenceacts as a reference sequence, to which test sequences are compared. Whenusing a sequence comparison algorithm, test and reference sequences areinput into a computer, subsequence coordinates are designated, ifnecessary, and sequence algorithm program parameters are designated. Thesequence comparison algorithm then calculates the percent sequenceidentity for the test sequence(s) relative to the reference sequence,based on the designated program parameters. Optimal alignment ofsequences for comparison can be conducted, e.g., by the local homologyalgorithm of Smith & Waterman (1981) Adv. Appl. Math. 2: 482, by thehomology alignment algorithm of Needleman & Wunsch (1970) J. Mol. Biol.48: 443, by the search for similarity method of Pearson & Lipman (1988)Proc. Natl. Acad. Sci., USA, 85: 2444, by computerized implementationsof these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the WisconsinGenetics Software Package, Genetics Computer Group, 575 Science Dr.,Madison, Wis.), or by visual inspection.

The term “specificity” when used with respect to the antimicrobialactivity of a peptide indicates that the peptide preferentially inhibitsgrowth and/or proliferation and/or kills a particular microbial speciesas compared to other related species. In certain embodiments thepreferential inhibition or killing is at least 10% greater (e.g., LD₅₀is 10% lower), preferably at least 20%, 30%, 40%, or 50%, morepreferably at least 2-fold, at least 5-fold, or at least 10-fold greaterfor the target species.

“Treating” or “treatment” of a condition as used herein may refer topreventing the condition, slowing the onset or rate of development ofthe condition, reducing the risk of developing the condition, preventingor delaying the development of symptoms associated with the condition,reducing or ending symptoms associated with the condition, generating acomplete or partial regression of the condition, or some combinationthereof.

The term “consisting essentially of” when used with respect to anantimicrobial peptide (AMP) or AMP motif as described herein, indicatesthat the peptide or peptides encompassed by the library or variants,analogues, or derivatives thereof possess substantially the same orgreater antimicrobial activity and/or specificity as the referencedpeptide. In certain embodiments substantially the same or greaterantimicrobial activity indicates at least 80%, preferably at least 90%,and more preferably at least 95% of the anti microbial activity of thereferenced peptide(s) against a particular bacterial species (e.g., S.mutans).

In various embodiments the amino acid abbreviations shown in Table 1 areused herein.

TABLE 1 Amino acid abbreviations. Abbreviation Name 3 Letter 1 LetterAlanine Ala A βAlanine (NH₂—CH₂—CH₂—COOH) βAla Arginine Arg R AsparagineAsn N Aspartic Acid Asp D Cysteine Cys C Glutamic Acid Glu E GlutamineGln Q Glycine Gly G Histidine His H Homoserine Hse — Isoleucine Ile ILeucine Leu L Lysine Lys K Methionine Met M Methionine sulfoxide Met (O)— Methionine methylsulfonium Met (S—Me) — Norleucine Nle — PhenylalaninePhe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp WTyrosine Tyr Y Valine Val V episilon-aminocaproic acid Ahx J(NH²—(CH₂)₅—COOH) 4-aminobutanoic acid gAbu (NH₂—(CH₂)₃—COOH)tetrahydroisoquinoline-3- O carboxylic acidLys(N(epsilon)-trifluoroacetyl) K[TFA] α-aminoisobutyric acid Aib B

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows alpha-helix wheel projections for representative peptidesfrom the binary and alpha-helix libraries. Residues are numberedconsecutively from the N terminus to the C terminus, with hydrophobicresidues shaded.

FIGS. 2A and 2B illustrate the comparative killing kinetics ofbinary-to-α-helix and binary-to-RW fusion peptides. S. mutans waschallenged with 25 μg/ml binary-to-α-helix (FIG. 2A) or binary-to-RW(FIG. 2B) fusion peptides or parent AMPs, and the surviving CFU wereplated at various time points post-addition. Samples at 0 min wereplated prior to peptide treatment. All data points represent the averageof results of at least three independent experiments±standarddeviations.

DETAILED DESCRIPTION

In various embodiments this invention pertains to the discovery of novelpeptides that have antimicrobial activity. In certain embodiments thepeptides are effective to kill and/or to inhibit growth and/orproliferation of Streptococcus mutans (S. mutans) and certain otherspecies (e.g., fungi [e.g., Candida albicans, etc.), Gram-negativebacteria [e.g., Pseudomonas aeruginosa, etc.], and Gram-positivebacteria [e.g., Enterococcus faecalis, Straphylococcus aureus,Lactobacillus, etc.).

S. mutans is a pathogen found in the oral cavity and is a majorcausative agent responsible for dental caries formation, one of the mostprevalent and costly bacterial infections worldwide (see, e.g., NationalInstitutes of Health (2000) Oral health in America: a report of theSurgeon General, Department of Health and Human Services, NationalInstitute of Dental and Craniofacial Research, National Institutes ofHealth, Bethesda, Md.; Washington State Department of Health (2002)Infectious Diseases—Dental Caries, Washington State Department ofHealth, Olympia, Wash.; Loesche (1986) Microbial Rev., 50: 353-380;Anderson and Shi (2006) Pediatr. Dent. 28: 151-153; discussion 192-198,and the like). The high financial burden of treating dental caries inthe U.S., especially among underprivileged and minority populations, aswell as evidence that indicates oral streptococci (including S. mutans)may directly contribute to more serious clinical consequences, such asheart disease (Doyuk et al. (2002) J. Infect 45: 39-41; Nakano et al.(2006) J. Clin. Microbiol., 44: 3313-3317), highlights the importance ofdeveloping additional therapeutics against this pathogen.

The antimicrobial peptides (AMPs) of this invention finds uses in alarge number of contexts. For example, the peptides can be systemicallyor locally administered to inhibit or eliminate infections comprising S.mutans and other strains or species. In certain embodiments theantimicrobial peptides can be incorporated into various healthcareproducts as well. For example, the peptides can be incorporated intotoothpaste or mouthwash to reduce or prevent colonization orrecolonization of the oral cavity and thereby reduce the incidenceand/or degree of dental carie formation. In various embodiments the AMPscan be incorporated into dental floss for similar purposes or can beprovided in swabs that are used to swab the teeth and oral mucosa.

In certain embodiments the AMPs can be incorporated into products as acomponent of a preservative to inhibit bacterial colonizationand/degradation of the product.

These uses are illustrative and not intended to be limiting. Using theteachings provided herein, one of skill will recognize that the peptidescan be used as active ingredient in an antimicrobial preparation foruses including, but not limited to surface treatment of articles tocounteract microbial growth on the said surface, and as additive inhuman and animal food, hygienic care products, disinfectants, cleaningagents, biocides, and the like.

I. Antimicrobial Peptides.

To avoid the synthesis of large combinatorial libraries of randompeptides, synthetic peptides with anti-S. mutans activity were producedby rationally designing several small structurally diverse peptidelibraries and then screening these libraries for S. mutans killingability. In certain embodiments each library was limited to peptides ofa defined size and structural framework, and the sequences within eachlibrary were varied incrementally to generate peptides with varyingbiochemical characteristics. These characteristics includedaromatidhydrophobic residue content, net positive charge, and predictedamphipathic, a-helix-forming character. One library was constructed bysystematically deleting residues from several active amphipathicsequences (see, e.g., Example 4). Another library was created bysubstituting histidines (His). These acid-activated peptides weredesigned to be active below pH 6.0 (see, e.g., Example 2).

To further improve the effectiveness of peptides exhibiting anti-S.mutans characteristics, the most bactericidal peptides from each librarywere synthesized together as one molecule, in various combinations andwith and without a flexible peptide linker between each antimicrobialregion, to generate fusion peptides. Many of these fusion peptides hadenhanced killing activities compared with the original non-conjoinedmolecules.

Accordingly, the results presented herein provide novel antimicrobialpeptides and a novel method of identifying additional antimicrobialpeptides using small rationally designed libraries. Interestingly, themost-active peptides derived in this study appear to be selective forseveral Gram-positive oral bacteria. As S. mutans normally grows in abiofilm state in vivo, we were encouraged to also find that thedescribed herein had activity against in vitro S. mutans biofilms grownon glass slides (data not shown).

Illustrative peptides are shown in Table 6 (binary library, alpha helixlibrary and RW library). In various embodiments, this inventioncontemplates concatamers of the peptides (integral or fractional, e.g.,as shown in Formula I, below) as well as chimeras comprising twopeptides joined together either directly, through a peptide linker, orchemically conjugated.

In certain embodiments (e.g., binary libraries and α-helix libraries)the antimicrobial peptides comprise the amino acid motif or circularpermutation of the amino acid motif of Formula I:

(H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵)_(n)

where n ranges from 1 to 5 and can increment by units of 0.1; H¹, H²,H³, H⁴, and H⁵ are independently selected hydrophobic or hydrophilicamino acids; C¹, C², C³, C⁴, and C⁵ are independently selectedpositively or negatively charged amino acids and/or, in certainembodiments, neutral amino acids; and the said peptide is effective tokill or inhibit the growth and/or proliferation of Streptococcus mutansin culture. In certain embodiments the peptide forms an alpha helix. Incertain embodiments the said peptide excludes the amino acid sequenceFKKFWKW FRRF (SEQ ID NO:31).

In formula I, n is said to increment by units of 0.1 to recognize thatthe motif may be partially repeated. This is illustrated in Table 2.

TABLE 2 Illustration of how motif is partially repeated as n incrementsby 0.1. Seq ID n Motif No 1 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ 7 1.1H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶ 8 1.2 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶ 9 1.3H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷ 10 1.4 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷ 11 1.5H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸ 12 1.6 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸13 1.7 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹ 14 1.8 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰ 15 1.9 H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰C⁹ 16 2H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰C⁹C¹⁰ 17

The superscript for H or C residues is incremented as new residues areadded (as n is increased) indicating that the new hydrophobic residue(H) is independently selected from the other hydrophobic residues andthe new charged or neutral residue (C) is independently selected fromthe other charged or neutral residues.

In certain embodiments, this invention contemplates circularpermutations of the peptides encompassed by Formula I. The circularpermutation of the motif simply indicates that the motif can begin withany residue. It is equivalent of joining the two ends of the motif(amino joined to carboxyl terminus) and then opening the circularizedpeptide at a different location. Of course the circularly permutedpeptide need not have been made in this matter, but merely have an aminoacid sequence or a motif equivalent to the sequence or motif produced bythis operation.

Table 3 illustrates various circular permutations of Formula I.

TABLE 3 Illustrative circular permutations (CPs) of Formula I. SEQFormula/ ID CP n Motif No Formula I H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ 18 n = 1 CP n =1 C¹C²H²H³C³H⁴H⁵C⁴C⁵H¹ 19 CP n = 1 H²H³C³H⁴H⁵C⁴C⁵ H¹C¹C² 20 CP n = 1H⁴H⁵C⁴C⁵ H¹C¹C²H²H³C³ 21 Formula I H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹22 n = 1.7 CP n = 1.7 H³C³H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹C¹C²H² 23 CP n = 1.7H⁴H⁵C⁴C⁵ H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹C¹C²H²H³C³ 24 CP n = 2H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰C⁹C¹⁰ 25 CP n = 2H⁵C⁴C⁵H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰C⁹C¹⁰H¹C¹C²H²H³C³H⁴ 26 Formula IH²H³C³H⁴H⁵C⁴C⁵H⁶C⁶C⁷H⁷H⁸C⁸H⁹H¹⁰C⁹C¹⁰H¹C¹C² 27 n = 2

In certain embodiments, charge is varied at the C positions by utilizinguncharged S, T, Y; positive K, R, H; or negative N, Q, D, E residues. Incertain embodiments hydrophobicity variation is controlled by using L,I, V, W, and F amino acids.

In certain embodiments the binary library peptides shown in Table 6include peptides according to Formula I where n is 1.1, while theα-helix library peptides include peptides according to Formula I, wheren is 1.4.

Also provided are RW library peptides (see, e.g., Table 6). In variousembodiments the RW library peptides are seven, eight, nine, ten, or 11amino acid peptides, of which all but 2 amino acids are Arg (R) or Trp(W) (or analogues or derivatives thereof) arranged in any combination.The no non-Arg or Trp RW residues are Lys or Phe or derivatives oranalogues thereof. In certain embodiments the peptides are seven residuepeptides all of which all but 2 amino acids are be Arg or Trp (arrangedin any combination). The two non-Arg or Trp residues are Lys or Phe orderivatives or analogues thereof. In various embodiments the N-terminalresidue of RW library peptides is arginine.

In certain embodiments, the peptides of this invention include, but arenot limited to acid activated peptides (see, e.g., Example 2), peptidesof the killing library #7 (see, e.g., Example 3), and beta-deletionlibraries (see, e.g., Example 4). Peptides within the Killing #7 andBeta-deletion libraries were constructed from a sequence framework,similar to that described above, of alternating clusters of hydrophobicand charged amino acids. For Killing Library #7, the maximum number ofamino acids was limited to 9 with, in certain embodiments, amidatedC-termini (see, e.g., Table 11). For the Beta-deletion Library (see,e.g., Table 12), we varied the size of the sequences from 15 to 7residues, though all the sequences were limited to equivalentamphipathic and hydrophobic characteristics (data not shown).

Histidine residues have a side-chain pKa near 6.0, and therefore carry acationic charge at pH 6.0 and below, but not at neutral pH. Weconstructed the Acid-activated Library with this characteristic in mind,so that an amphipathic, helix forming arrangement (leading to anti-S.mutans activity) would result in a low pH environment (such as thatcreated by S. mutans on a carious lesion), but the peptides would remaininactive above pH 6.0. 42. Accordingly, in certain embodiments, theactive antimicrobial peptides comprise an acid-activated amphipathichelical peptide ranging in length from about 7 to about 11 amino acidswhere the majority of charged residues are His or a derivative oranalogue thereof that caries a cationic charge at an acidic pH. Thepeptide typically has little or substantially no antimicrobial activityat neutral pH (e.g., against S. mutans), but has antimicrobial activity(e.g., against S. mutans) at an acidic pH (e.g., a pH of about 6 orlower, e.g., from about pH 1.4 to about pH 6, from about pH 2, about pH3, about pH4, or about pH 5 to about pH 6, or about pH 6.5). In certainembodiments all charged residues in these peptides are His or aderivative or analogue thereof that caries a cationic charge at anegative pH. Certain acid-activated peptides comprises alternatingrepeats of HH and FF. In certain embodiments the peptide additionallythe amino acid sequence KLLK (SEQ ID NO:166), or conservativesubstitutions thereof, at one or both termini. In certain embodimentsthe peptides further comprise peptide comprises the amino acid sequenceKLLK (SEQ ID NO:166), or conservative substitutions thereof, at one orboth termini where the KLLK (SEQ ID NO:166), is joined to the terminusby a linker (e.g., GAT (SEQ ID NO:167). Various acid-activated peptidescomprise the amino acid sequence FHFFHHFFHFFHHF (SEQ ID NO:168). Anumber of acid activated AMPs are illustrated in Example 2 (see, e.g.Table 10).

In various embodiments any of the peptides described herein can comprisenaturally occurring amino acids, or non-naturally occurring amino acidsincluding derivatives and analogues of naturally occurring amino acids.In addition, various peptides an include L-form amino acids, D-formamino acids, and/or beta-amino acids.

It will also be appreciated in addition to the D-form and L-form andbeta-peptide sequences expressly illustrated herein, this invention alsocontemplates retro and retro-inverso forms of each of these peptides. Inretro forms, the direction of the sequence is reversed. In inverseforms, the chirality of the constituent amino acids is reversed (i.e., Lform amino acids become D form amino acids and D form amino acids becomeL form amino acids). In the retro-inverso form, both the order and thechirality of the amino acids is reversed. Thus, for example, a retroform of the of the peptide B-36 (RLLKRFKHLFK, SEQ ID NO:34) has thesequence KFLHKFRKLLR (SEQ ID NO:28). Where the B-36 peptide comprisesall L amino acids, the inverse form will comprise all D amino acids andthe retro-inverso (retro-inverse) form will have the sequence of SEQ IDNO:28 comprise all D form amino acids.

In various embodiments, any of the peptides described herein, can bearone or more protecting groups. Thus, for example, the carboxyl terminuscan be amidated. In various embodiments certain termini and/or sidechains bear one or more blocking groups. the C-terminus, and/orN-terminus, and/or internal residues can be blocked with one or moreblocking groups as described herein.

A wide number of protecting groups are suitable for this purpose. Suchgroups include, but are not limited to acetyl, amide, and alkyl groupswith acetyl and alkyl groups being particularly preferred for N-terminalprotection and amide groups being preferred for carboxyl terminalprotection. In certain embodiments, the protecting groups include, butare not limited to alkyl chains as in fatty acids, propeonyl, formyl,and others. Certain preferred carboxyl protecting groups include, butare not limited to amides, esters, and ether-forming protecting groups.In one embodiment, an acetyl group can be used to protect the aminoterminus and an amide group can be used to protect the carboxylterminus. These blocking groups enhance the helix-forming tendencies ofthe peptides. Certain particularly preferred blocking groups includealkyl groups of various lengths, e.g., groups having the formula:CH₃—(CH₂)_(n)—CO— where n ranges from about 1 to about 20, preferablyfrom about 1 to about 16 or 18, more preferably from about 3 to about13, and most preferably from about 3 to about 10.

Other suitable protecting groups include, but are not limited to Fmoc,t-butoxycarbonyl (t-BOC), 9-fluoreneacetyl group, 1-fluorenecarboxylicgroup, 9-florenecarboxylic group, 9-fluorenone-1-carboxylic group,benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt),4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr),Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl(Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pmc), 4-methylbenzyl(MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl),Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys),1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl(2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z),2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom), cyclohexyloxy(cHxO), t-butoxymethyl (Bum), t-butoxy (tBuO), t-Butyl (tBu), Acetyl(Ac), and Trifluoroacetyl (TFA), and the like.

Protecting/blocking groups are well known to those of skill as aremethods of coupling such groups to the appropriate residue(s) comprisingthe peptides of this invention (see, e.g., Greene et al., (1991)Protective Groups in Organic Synthesis, 2nd ed., John Wiley & Sons, Inc.Somerset, N.J.). In one embodiment, for example, acetylation isaccomplished during the synthesis when the peptide is on the resin usingacetic anhydride. Amide protection can be achieved by the selection of aproper resin for the synthesis. For example, synthesis of the peptidesdescribed herein can be performed using rink amide resin as the solidsupport. After the completion of the synthesis, the semipermanentprotecting groups on acidic bifunctional amino acids such as Asp and Gluand basic amino acid Lys, hydroxyl of Tyr can be simultaneously removed.The peptides released from such a resin using acidic treatment come outwith the n-terminal protected as acetyl and the carboxyl protected asNH₂ and with the simultaneous removal of all of the other protectinggroups.

In various embodiments this invention also contemplates pegylated formsof the various protected or unprotected L-form, D-form, beta-, retro-,inverse, and/or retro-inverso peptides of this invention. Pegylation canbe used in improve biocompatibility of the peptides and/or to improveserum half-life. Methods of pegylating peptides are well known to thoseof skill in the art (see, e.g., U.S. Pat. Nos. 7,256,258, 6,552,170, and6,420,339, and the references cited therein).

For the binary, killing peptide #7, beta-deletion, and α-helixlibraries, described herein, results indicated that maximal S. mutansactivity occurred in peptides with both high relative hydrophobicity andover +3 net positive charge. Intermediate levels of activity wereobserved for peptides whose properties were dominated by either singletrait. These results are consistent with what is known of most syntheticand natural AMPs with cationic amphipathic character, and suggest thatB-33, α-7 and the other active sequences in these libraries may behavein a manner similar to other AMPs; i.e., the positive charge of thepeptide provides for AMP attraction to anionic bacterial membranes,while the amphipathicity is facilitates membrane interaction, helixtransition, and cell killing (Hancock and Lehrer (1998) TrendsBiotechnol., 16: 82-88; Shai (1999) Biochim Biophys Acta 1462: 55-70).These results also indicate that a high <Helix> value, on its own, maynot correlate with increased anti-S. mutans activity for cationicamphipathic AMPs. However, at pH 6.0, some peptides within theAcid-activated library have strong amphipathic helix forming characterthat seems to correlate with an increased relative His content andactivity against S. mutans.

For the RW Library, as was the case with the Binary and a-helixlibraries, the most hydrophobic and cationic sequences were the mostactive (2C-3, -4). Despite the differences in length and periodicitycompared with peptides in the other libraries, RW peptides can gainenhanced activity from improvements in initial peptide binding ormembrane insertion. Without being bound to a particular theory, it isbelieved that Arg and Trp-rich peptides, despite their low <Helix>values, form stable helix-like amphipathic arrangements upon membraneinteraction that are stabilized by electrostatic bonds between the Trp Helectrons and the Arg functional group (see, e.g., Mecozzi et al. (1996)Proc. Natl. Acad. Sci., USA, 93: 10566-10571; Jing et al. (2003) J.Pept. Res. 61: 219-229). Thus, the unique sequence properties of the RWLibrary peptides allow them to obtain secondary structures that arehighly conducive to antimicrobial activity.

In various embodiments, this invention contemplates concatamerscomprising combinations of two or more different peptides of thisinvention joined together directly or through a linker (e.g., peptidelinker, or other linker). Thus, chemical conjugates are contemplated aswell as fusion proteins. The results provided herein indicate thatfusion peptides, AMP dinners synthesized as single linear molecules,often have increased killing kinetics compared to their parentalpeptides. Some fusion peptides may function by increasing the number ofhelix-forming units per molecule at the membrane surface, as has beendescribed for bundled AMPs (see, e.g., Sal-Man et al. (2002)Biochemistry 41: 11921-11930). Furthermore, the results presented hereinsuggest that the effect of constituent arrangement (which fusion peptidesubunit goes at the C or N terminal) may be difficult to predict(compare the MICs of FBα-12 and FB§-20), though other work hasdemonstrated that amphipathic and putative helix-forming AMPs appear tobe more tolerant of N-terminal additions (Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 3833-3838; Szynol et al. (2006) ChemBiol Drug Des 67: 425-431).

Overall, the results provided herein show that S. mutans are susceptibleto AMPs with relatively high hydrophobicity and cationic charge, whichcan be readily isolated from libraries using the methods providedherein. Additionally, fusion peptides constructed from conjoining activesequences from within and between these libraries improve the killingkinetics of these peptides.

The AMPs provided herein are believed to be effective against microbialinfection at normally sterile and mucosal surfaces, even when theinfections are caused by antibiotic resistant strains. The AMPs can bedelivered topically by any number of conventional methods.Alternatively, they can delivered systemically by, for example, oraladministration or injection. The rationally-designed AMPs providedherein are small (most under 20 amino acids), and are therefore easy tochemically synthesize at high yield, an improvement over other syntheticAMPs that are significantly longer (30-40 amino acids) and moredifficult to construct and purify. The AMPs provided can also be easilytailored for protease resistance, for example by incorporation ofD-isomer amino acids, by pegylation, by use of non-naturally occurringamino acids, and the like.

II. Peptide Preparation.

Peptide Preparation.

The peptides used in this invention can be chemically synthesized usingstandard chemical peptide synthesis techniques or, particularly wherethe peptide does not comprise “D” amino acid residues, the peptide canbe recombinantly expressed. Where the “D” polypeptides are recombinantlyexpressed, a host organism (e.g. bacteria, plant, fungal cells, etc.)can be cultured in an environment where one or more of the amino acidsis provided to the organism exclusively in a D form. Recombinantlyexpressed peptides in such a system then incorporate those D aminoacids.

In certain embodiments, D amino acids can be incorporated inrecombinantly expressed peptides using modified amino acyl-tRNAsynthetases that recognize D-amino acids.

In certain embodiments the peptides are chemically synthesized by any ofa number of fluid or solid phase peptide synthesis techniques known tothose of skill in the art. Solid phase synthesis in which the C-terminalamino acid of the sequence is attached to an insoluble support followedby sequential addition of the remaining amino acids in the sequence is apreferred method for the chemical synthesis of the polypeptides of thisinvention. Techniques for solid phase synthesis are well known to thoseof skill in the art and are described, for example, by Barany andMerrifield (1963) Solid-Phase Peptide Synthesis; pp. 3-284 in ThePeptides: Analysis, Synthesis, Biology. Vol. 2: Special Methods inPeptide Synthesis, Part A.; Merrifield et al. (1963) J. Am. Chem. Soc.,85: 2149-2156, and Stewart et al. (1984) Solid Phase Peptide Synthesis,2nd ed. Pierce Chem. Co., Rockford, Ill.

In one embodiment, the peptides can be synthesized by the solid phasepeptide synthesis procedure using a benzhyderylamine resin (BeckmanBioproducts, 0.59 mmol of NH₂/g of resin) as the solid support. The COOHterminal amino acid (e.g., t-butylcarbonyl-Phe) is attached to the solidsupport through a 4-(oxymethyl)phenacetyl group. This is a more stablelinkage than the conventional benzyl ester linkage, yet the finishedpeptide can still be cleaved by hydrogenation. Transfer hydrogenationusing formic acid as the hydrogen donor can be used for this purpose.Detailed protocols for peptide synthesis and analysis of synthesizedpeptides are described in a miniprint supplement accompanyingAnantharamaiah et al. (1985) J. Biol. Chem., 260(16): 10248-10255.

It is noted that in the chemical synthesis of peptides, particularlypeptides comprising D amino acids, the synthesis usually produces anumber of truncated peptides in addition to the desired full-lengthproduct. Thus, the peptides are typically purified using, e.g., HPLC.

D-amino acids, beta amino acids, non-natural amino acids, and the likecan be incorporated at one or more positions in the peptide simply byusing the appropriately derivatized amino acid residue in the chemicalsynthesis. Modified residues for solid phase peptide synthesis arecommercially available from a number of suppliers (see, e.g., AdvancedChem Tech, Louisville; Nova Biochem, San Diego; Sigma, St Louis; BachemCalifornia Inc., Torrance, etc.). The D-form and/or otherwise modifiedamino acids can be completely omitted or incorporated at any position inthe peptide as desired. Thus, for example, in certain embodiments, thepeptide can comprise a single modified acid, while in other embodiments,the peptide comprises at least two, generally at least three, moregenerally at least four, most generally at least five, preferably atleast six, more preferably at least seven or even all modified aminoacids. In certain embodiments, essentially every amino acid is a D-formamino acid.

As indicated above, the peptides or fusion proteins of this inventioncan also be recombinantly expressed.

In a certain embodiments, the antimicrobial peptides of this inventionare synthesized using recombinant expression systems. Generally thisinvolves creating a DNA sequence that encodes the desired peptide orfusion protein, placing the DNA in an expression cassette under thecontrol of a particular promoter, expressing the peptide or fusionprotein in a host, isolating the expressed peptide or fusion proteinand, if required, renaturing the peptide or fusion protein.

DNA encoding the peptide(s) or fusion protein(s) described herein can beprepared by any suitable method as described above, including, forexample, cloning and restriction of appropriate sequences or directchemical synthesis.

This nucleic acid can be easily ligated into an appropriate vectorcontaining appropriate expression control sequences (e.g. promoter,enhancer, etc.), and, optionally, containing one or more selectablemarkers (e.g. antibiotic resistance genes).

The nucleic acid sequences encoding the peptides or fusion proteins ofthis invention can be expressed in a variety of host cells, including,but not limited to, E. coli, other bacterial hosts, yeast, fungus, andvarious higher eukaryotic cells such as insect cells (e.g. SF3), theCOS, CHO and HeLa cells lines and myeloma cell lines. The recombinantprotein gene will typically be operably linked to appropriate expressioncontrol sequences for each host. For E. coli this can include a promotersuch as the T7, trp, or lambda promoters, a ribosome binding site andpreferably a transcription termination signal. For eukaryotic cells, thecontrol sequences can include a promoter and often an enhancer (e.g., anenhancer derived from immunoglobulin genes, SV40, cytomegalovirus,etc.), and a polyadenylation sequence, and may include splice donor andacceptor sequences.

The plasmids of the invention can be transferred into the chosen hostcell by well-known methods such as calcium chloride transformation forE. coli and calcium phosphate treatment or electroporation for mammaliancells. Cells transformed by the plasmids can be selected by resistanceto antibiotics conferred by genes contained on the plasmids, such as theamp, gpt, neo and hyg genes.

Once expressed, the recombinant peptide(s) or fusion protein(s) can bepurified according to standard procedures of the art, including ammoniumsulfate precipitation, affinity columns, column chromatography, gelelectrophoresis and the like (see, generally, R. Scopes, (1982) ProteinPurification, Springer-Verlag, N.Y.; Deutscher (1990) Methods inEnzymology Vol. 182: Guide to Protein Purification., Academic Press,Inc. N.Y.). Substantially pure compositions of at least about 90 to 95%homogeneity are preferred, and 98 to 99% or more homogeneity are mostpreferred.

One of skill in the art would recognize that after chemical synthesis,biological expression, or purification, the peptide(s) or fusionprotein(s) of this invention may possess a conformation substantiallydifferent than desired native conformation. In this case, it may benecessary to denature and reduce the peptide or fusion protein and thento cause the molecule to re-fold into the preferred conformation.Methods of reducing and denaturing proteins and inducing re-folding arewell known to those of skill in the art (see, e.g., Debinski et al.(1993) J. Biol. Chem., 268: 14065-14070; Kreitman and Pastan (1993)Bioconjug. Chem., 4: 581-585; and Buchner, et al., (1992) Anal.Biochem., 205: 263-270). Debinski et al., for example, describes thedenaturation and reduction of inclusion body proteins in guanidine-DTE.The protein is then refolded in a redox buffer containing oxidizedglutathione and L-arginine.

One of skill would recognize that modifications can be made to thepeptide(s) and/or fusion protein(s) proteins without diminishing theirbiological activity. Some modifications may be made to facilitate thecloning, expression, or incorporation of the targeting molecule into afusion protein. Such modifications are well known to those of skill inthe art and include, for example, a methionine added at the aminoterminus to provide an initiation site, or additional amino acids (e.g.,poly His) placed on either terminus to create conveniently locatedrestriction sites or termination codons or purification sequences.

Compound Peptide Preparation.

In certain embodiments this invention contemplates the use of “compound’antimicrobial peptides comprising two or more antimicrobial peptides(AMPs) joined together. The peptides can be joined directly or through alinker. In various embodiments the AMPs are chemically conjugated oralternatively, where they are directly linked or linked through apeptide linker the compound AMPs can be expressed as a fusion protein.

Typically the compounds AMPs will include at least one AMP describedherein attached to a second AMP. The second AMP can be an AMP asdescribed herein, or other AMPs known to those of skill in the art. Anumber of different AMPs are know to those of skill in the art (see,e.g., U.S. Pat. Nos. 7,271,239, 7,223,840, 7,176,276, 6,809,181,6,699,689, 6,420,116, 6,358,921, 6,316,594, 6,235,973, 6,183,992,6,143,498, 6,042,848, 6,040,291, 5,936,063, 5,830,993, 5,428,016,5,424,396, 5,032,574, 4,623,733, which are incorporated herein byreference for the disclosure of particular AMPs).

In certain embodiments the compound AMPs comprise two or more AMPs ofthe present invention attached to each other.

In one embodiment, the a AMPs are chemically conjugated to each other.Means of chemically conjugating molecules are well known to those ofskill. Peptides typically contain variety of functional groups; e.g.,carboxylic acid (COOH) or free amine (—NH₂) groups, that are availablefor reaction with a suitable functional group(s) to bind each other.

Alternatively, peptide(s) can be derivatized to expose or attachadditional reactive functional groups. The derivatization can involveattachment of any of a number of linker molecules such as thoseavailable from Pierce Chemical Company, Rockford Ill.

A “linker”, as used herein, is a molecule that is used to join twomolecules The linker is typically capable of forming covalent bonds toboth molecule(s) (e.g., AMPs). Suitable linkers are well known to thoseof skill in the art and include, but are not limited to, straight orbranched-chain carbon linkers, heterocyclic carbon linkers, or peptidelinkers. In certain embodiments the linkers can be joined to theconstituent amino acids through their side groups (e.g., through adisulfide linkage to cysteine). However, in certain preferredembodiments, the linkers will be joined to the alpha carbon amino andcarboxyl groups of the terminal amino acids.

A bifunctional linker having one functional group reactive with a groupon one molecule (e.g., AMP), and another group reactive on the othermolecule (e.g., different AMP), can be used to form the desiredconjugate. Alternatively, derivatization be performed to providefunctional groups. Thus, for example, procedures for the generation offree sulfhydryl groups on peptides are also known (See U.S. Pat. No.4,659,839).

Many procedures and linker molecules for attachment of various moleculesto peptides or proteins are known (see, e.g., European PatentApplication No. 188,256; U.S. Pat. Nos. 4,671,958, 4,659,839, 4,414,148,4,699,784; 4,680,338; 4,569,789; and 4,589,071; and Borlinghaus et al.(1987) Cancer Res. 47: 4071-4075).

Where the AMPs are directly linked or joined by a peptide linker, theycan be synthesized using standard chemical peptide synthesis techniques.Where both components are relatively short the chimeric moiety can besynthesized as a single contiguous polypeptide. Alternatively themolecules can be synthesized separately and then fused by condensationof the amino terminus of one molecule with the carboxyl terminus of theother molecule thereby forming a peptide bond. Alternatively, AMPs canbe each be condensed with one end of a peptide spacer molecule therebyforming a contiguous fusion protein.

In certain embodiments, the compound AMPs are synthesized as fusionproteins using recombinant DNA methodology. Generally this involvescreating a DNA sequence that encodes the fusion protein, placing the DNAin an expression cassette under the control of a particular promoter,expressing the protein in a host, isolating the expressed protein and,if required, renaturing the protein. Methods of generating fusionproteins are known to those of skill in the art.

In various embodiments a peptide linker is used to join each of theAMPs. In various embodiments the peptide linker is relatively short,typically less than about 10 amino acids, preferably less than about 8amino acids and more preferably about 3 to about 5 amino acids. Suitableillustrative linkers include, but are not limited to PSGSP (SEQ IDNO:106), ASASA (SEQ ID NO:107), or GGG (SEQ ID NO:108). In certainembodiments longer linkers such as (GGGGS)₃ (SEQ ID NO:29) can be used.

In certain embodiments this invention contemplates attaching the AMPs ofthis invention or the compound AMPs to a targeting moiety (e.g., abacteria-specific peptide or antibody) to improve the specificity of theAMP. Illustrative antibodies and/or peptide targeting moieties aredescribed for example, in U.S. Ser. No. 10/706,391, published as US2004/0137482, and the like.

The targeting moiety can be chemically conjugated to the AMP or compoundAMP or the chimeric moiety can be expressed as a fusion protein, e.g.,as explained above for the fabrication of compound AMPs.

Peptide Labeling.

In various embodiments the antimicrobial peptide(s) described hereinand/or the compound AMPs described herein are labeled with a detectablelabel. Detectable labels suitable for use in the present inventioninclude any composition detectable by spectroscopic, photochemical,biochemical, immunochemical, electrical, optical or chemical means.Useful labels in the present invention include, but are not limited tobiotin for staining with labeled streptavidin conjugate, magnetic beads(e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red,rhodamine, green fluorescent protein, quantum dots, and the like, see,e.g., Molecular Probes, Eugene, Oreg., USA), radiolabels (e.g., ³H,¹²⁵I, ³⁵S, ¹⁴C, or ³²P), enzymes (e.g., horse radish peroxidase,alkaline phosphatase and others commonly used in an ELISA), andcolorimetric labels such as colloidal gold (e.g., gold particles in the40-80 nm diameter size range scatter green light with high efficiency)or colored glass or plastic (e.g., polystyrene, polypropylene, latex,etc.) beads. Patents teaching the use of such labels include U.S. Pat.Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149;and 4,366,241.

In certain embodiments fluorescent labels are preferred because theyprovides a very strong signal with low background and entail noradioactivity. They are also optically detectable at high resolution andsensitivity through a quick scanning procedure.

Suitable chromogens that can be employed include those molecules andcompounds that absorb light in a distinctive range of wavelengths sothat a color can be observed or, alternatively, that emit light whenirradiated with radiation of a particular wave length or wave lengthrange, e.g., fluorescers.

Desirably, fluorescent labels should absorb light above about 300 nm,preferably about 350 nm, and more preferably above about 400 nm, usuallyemitting at wavelengths greater than about 10 nm higher than thewavelength of the light absorbed. It should be noted that the absorptionand emission characteristics of the bound dye can differ from theunbound dye. Therefore, when referring to the various wavelength rangesand characteristics of the dyes, it is intended to indicate the dyes asemployed and not the dye which is unconjugated and characterized in anarbitrary solvent.

Detectable signal can also be provided by chemiluminescent andbioluminescent sources. Chemiluminescent sources include a compoundwhich becomes electronically excited by a chemical reaction and can thenemit light which serves as the detectable signal or donates energy to afluorescent acceptor. Alternatively, luciferins can be used inconjunction with luciferase or lucigenins to provide bioluminescence.

Spin labels are provided by reporter molecules with an unpaired electronspin which can be detected by electron spin resonance (ESR)spectroscopy. Illustrative spin labels include, but are not limited toorganic free radicals, transitional metal complexes, particularlyvanadium, copper, iron, and manganese, and the like. Exemplary spinlabels include nitroxide free radicals.

The labels can be attached to the AMP directly or through a linkermoiety. In general, the site of label or linker-label attachment is notlimited to any specific position. For example, a label may be attachedto an amino acid side chain, or to the amino or carboxyl terminus of aterminal residue typically at any position that does not interfere withthe activity and/or specificity of the peptide.

It will be recognized that fluorescent labels are not to be limited tosingle species organic molecules, but include inorganic molecules,multi-molecular mixtures of organic and/or inorganic molecules,crystals, heteropolymers, and the like. Thus, for example, CdSe—CdScore-shell nanocrystals enclosed in a silica shell can be easilyderivatized for coupling to a biological molecule (Bruchez et al. (1998)Science, 281: 2013-2016). Similarly, highly fluorescent quantum dots(zinc sulfide-capped cadmium selenide) have been covalently coupled tobiomolecules for use in ultrasensitive biological detection (Warren andNie (1998) Science, 281: 2016-2018).

III. Formulations.

Pharmaceutical Formulations.

In order to carry out the methods of the invention, one or more activeagents (e.g., antimicrobial peptides (AMPS) or compound antimicrobialpeptides described herein) are administered to a mammal in need thereof,e.g., to a mammal suffering from a microbial infection orprophylactically to prevent a microbial infection and/or to prevent orreduce the incidence or severity of dental caries.

The active agent(s) can be administered in the “native” form or, ifdesired, in the form of salts, esters, amides, prodrugs, derivatives,and the like, provided the salt, ester, amide, prodrug or derivative issuitable pharmacologically, i.e., effective in the present method(s).Salts, esters, amides, prodrugs and other derivatives of the activeagents can be prepared using standard procedures known to those skilledin the art of synthetic organic chemistry and described, for example, byMarch (1992) Advanced Organic Chemistry; Reactions, Mechanisms andStructure, 4th Ed. N.Y. Wiley-Interscience.

Methods of formulating such derivatives are known to those of skill inthe art. For example, the disulfide salts of a number of delivery agentsare described in PCT Publication WO 00/059863 which is incorporatedherein by reference. Similarly, acid salts of therapeutic peptides,peptoids, or other mimetics, and can be prepared from the free baseusing conventional methodology that typically involves reaction with asuitable acid. Generally, the base form of the drug is dissolved in apolar organic solvent such as methanol or ethanol and the acid is addedthereto. The resulting salt either precipitates or can be brought out ofsolution by addition of a less polar solvent. Suitable acids forpreparing acid addition salts include, but are not limited to bothorganic acids, e.g., acetic acid, propionic acid, glycolic acid, pyruvicacid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid,fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid,mandelic acid, methanesulfonic acid, ethanesulfonic acid,p-toluenesulfonic acid, salicylic acid, and the like, as well asinorganic acids, e.g., hydrochloric acid, hydrobromic acid, sulfuricacid, nitric acid, phosphoric acid, and the like. An acid addition saltcan be reconverted to the free base by treatment with a suitable base.Certain particularly preferred acid addition salts of the active agentsherein include halide salts, such as may be prepared using hydrochloricor hydrobromic acids. Conversely, preparation of basic salts of theactive agents of this invention are prepared in a similar manner using apharmaceutically acceptable base such as sodium hydroxide, potassiumhydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine, or thelike. Particularly preferred basic salts include alkali metal salts,e.g., the sodium salt, and copper salts.

Preparation of esters typically involves functionalization of hydroxyland/or carboxyl groups that are present within the molecular structureof the active agent. In certain embodiments, the esters are typicallyacyl-substituted derivatives of free alcohol groups, i.e., moieties thatare derived from carboxylic acids of the formula RCOOH where R is alky,and preferably is lower alkyl. Esters can be reconverted to the freeacids, if desired, by using conventional hydrogenolysis or hydrolysisprocedures.

Amides can also be prepared using techniques known to those skilled inthe art or described in the pertinent literature. For example, amidesmay be prepared from esters, using suitable amine reactants, or they maybe prepared from an anhydride or an acid chloride by reaction withammonia or a lower alkyl amine.

In various embodiments, the active agents identified herein are usefulfor parenteral, topical, oral, nasal (or otherwise inhaled), rectal, orlocal administration, such as by aerosol or transdermally, forprophylactic and/or therapeutic treatment of infection (e.g., microbialinfection) one or more of the pathologies/indications described herein(e.g., atherosclerosis and/or symptoms thereof). The pharmaceuticalcompositions can be administered in a variety of unit dosage formsdepending upon the method of administration. Suitable unit dosage forms,include, but are not limited to powders, tablets, pills, capsules,lozenges, suppositories, patches, nasal sprays, injectibles, implantablesustained-release formulations, lipid complexes, etc.

The active agents of this invention can also be combined with apharmaceutically acceptable carrier (excipient) to form apharmacological composition. Pharmaceutically acceptable carriers cancontain one or more physiologically acceptable compound(s) that act, forexample, to stabilize the composition or to increase or decrease theabsorption of the active agent(s). Physiologically acceptable compoundscan include, for example, carbohydrates, such as glucose, sucrose, ordextrans, antioxidants, such as ascorbic acid or glutathione, chelatingagents, low molecular weight proteins, protection and uptake enhancerssuch as lipids, compositions that reduce the clearance or hydrolysis ofthe active agents, or excipients or other stabilizers and/or buffers.

Other physiologically acceptable compounds, particularly of use in thepreparation of tablets, capsules, gel caps, and the like include, butare not limited to binders, diluent/fillers, disentegrants, lubricants,suspending agents, and the like.

In certain embodiments, to manufacture an oral dosage form (e.g., atablet), an excipient (e.g., lactose, sucrose, starch, mannitol, etc.),an optional disintegrator (e.g. calcium carbonate,carboxymethylcellulose calcium, sodium starch glycollate, crospovidoneetc.), a binder (e.g. alpha-starch, gum arabic, microcrystallinecellulose, carboxymethylcellulose, polyvinylpyrrolidone,hydroxypropylcellulose, cyclodextrin, etc.), and an optional lubricant(e.g., talc, magnesium stearate, polyethylene glycol 6000, etc.), forinstance, are added to the active component or components (e.g., activepeptide and salicylanilide) and the resulting composition is compressed.Where necessary the compressed product is coated, e.g., known methodsfor masking the taste or for enteric dissolution or sustained release.Suitable coating materials include, but are not limited toethyl-cellulose, hydroxymethylcellulose, polyoxyethylene glycol,cellulose acetate phthalate, hydroxypropylmethylcellulose phthalate, andEudragit (Rohm & Haas, Germany; methacrylic-acrylic copolymer).

Other physiologically acceptable compounds include wetting agents,emulsifying agents, dispersing agents or preservatives that areparticularly useful for preventing the growth or action ofmicroorganisms. Various preservatives are well known and include, forexample, phenol and ascorbic acid. One skilled in the art wouldappreciate that the choice of pharmaceutically acceptable carrier(s),including a physiologically acceptable compound depends, for example, onthe route of administration of the active agent(s) and on the particularphysio-chemical characteristics of the active agent(s).

In certain embodiments the excipients are sterile and generally free ofundesirable matter. These compositions can be sterilized byconventional, well-known sterilization techniques. For various oraldosage form excipients such as tablets and capsules sterility is notrequired. The USP/NF standard is usually sufficient.

In therapeutic applications, the compositions of this invention areadministered, e.g., topically administered or administered to the oralor nasal cavity, to a patient suffering from infection or at risk forinfection or prophylactically to prevent dental caries or otherpathologies of the teeth or oral mucosa characterized by microbialinfection in an amount sufficient to prevent and/or cure and/or at leastpartially prevent or arrest the disease and/or its complications. Anamount adequate to accomplish this is defined as a “therapeuticallyeffective dose.” Amounts effective for this use will depend upon theseverity of the disease and the general state of the patient's health.Single or multiple administrations of the compositions may beadministered depending on the dosage and frequency as required andtolerated by the patient. In any event, the composition should provide asufficient quantity of the active agents of the formulations of thisinvention to effectively treat (ameliorate one or more symptoms in) thepatient.

The concentration of active agent(s) can vary widely, and will beselected primarily based on activity of the active ingredient(s), bodyweight and the like in accordance with the particular mode ofadministration selected and the patient's needs. Concentrations,however, will typically be selected to provide dosages ranging fromabout 0.1 or 1 mg/kg/day to about 50 mg/kg/day and sometimes higher.Typical dosages range from about 3 mg/kg/day to about 3.5 mg/kg/day,preferably from about 3.5 mg/kg/day to about 7.2 mg/kg/day, morepreferably from about 7.2 mg/kg/day to about 11.0 mg/kg/day, and mostpreferably from about 11.0 mg/kg/day to about 15.0 mg/kg/day. In certainpreferred embodiments, dosages range from about 10 mg/kg/day to about 50mg/kg/day. In certain embodiments, dosages range from about 20 mg toabout 50 mg given orally twice daily. It will be appreciated that suchdosages may be varied to optimize a therapeutic and/or phophylacticregimen in a particular subject or group of subjects.

In certain embodiments, the active agents of this invention areadministered to the oral cavity. This is readily accomplished by the useof lozenges, aerosol sprays, mouthwash, coated swabs, and the like.

In certain embodiments, the active agent(s) of this invention areadministered topically, e.g., to the skin surface, to a topical lesionor wound, to a surgical site, and the like.

In certain embodiments the active agents of this invention areadministered systemically (e.g., orally, or as an injectable) inaccordance with standard methods well known to those of skill in theart. In other preferred embodiments, the agents, can also be deliveredthrough the skin using conventional transdermal drug delivery systems,i.e., transdermal “patches” wherein the active agent(s) are typicallycontained within a laminated structure that serves as a drug deliverydevice to be affixed to the skin. In such a structure, the drugcomposition is typically contained in a layer, or “reservoir,”underlying an upper backing layer. It will be appreciated that the term“reservoir” in this context refers to a quantity of “activeingredient(s)” that is ultimately available for delivery to the surfaceof the skin. Thus, for example, the “reservoir” may include the activeingredient(s) in an adhesive on a backing layer of the patch, or in anyof a variety of different matrix formulations known to those of skill inthe art. The patch may contain a single reservoir, or it may containmultiple reservoirs.

In one embodiment, the reservoir comprises a polymeric matrix of apharmaceutically acceptable contact adhesive material that serves toaffix the system to the skin during drug delivery. Examples of suitableskin contact adhesive materials include, but are not limited to,polyethylenes, polysiloxanes, polyisobutylenes, polyacrylates,polyurethanes, and the like. Alternatively, the drug-containingreservoir and skin contact adhesive are present as separate and distinctlayers, with the adhesive underlying the reservoir which, in this case,may be either a polymeric matrix as described above, or it may be aliquid or hydrogel reservoir, or may take some other form. The backinglayer in these laminates, which serves as the upper surface of thedevice, preferably functions as a primary structural element of the“patch” and provides the device with much of its flexibility. Thematerial selected for the backing layer is preferably substantiallyimpermeable to the active agent(s) and any other materials that arepresent.

Other formulations for topical delivery include, but are not limited to,ointments, gels, sprays, fluids, and creams. Ointments are semisolidpreparations that are typically based on petrolatum or other petroleumderivatives. Creams containing the selected active agent are typicallyviscous liquid or semisolid emulsions, often either oil-in-water orwater-in-oil. Cream bases are typically water-washable, and contain anoil phase, an emulsifier and an aqueous phase. The oil phase, alsosometimes called the “internal” phase, is generally comprised ofpetrolatum and a fatty alcohol such as cetyl or stearyl alcohol; theaqueous phase usually, although not necessarily, exceeds the oil phasein volume, and generally contains a humectant. The emulsifier in a creamformulation is generally a nonionic, anionic, cationic or amphotericsurfactant. The specific ointment or cream base to be used, as will beappreciated by those skilled in the art, is one that will provide foroptimum drug delivery. As with other carriers or vehicles, an ointmentbase should be inert, stable, nonirritating and nonsensitizing.

As indicated above, various buccal, and sublingual formulations are alsocontemplated.

In certain embodiments, one or more active agents of the presentinvention can be provided as a “concentrate”, e.g., in a storagecontainer (e.g., in a premeasured volume) ready for dilution, or in asoluble capsule ready for addition to a volume of water, alcohol,hydrogen peroxide, or other diluent.

While the invention is described with respect to use in humans, it isalso suitable for animal, e.g., veterinary use. Thus certain preferredorganisms include, but are not limited to humans, non-human primates,canines, equines, felines, porcines, ungulates, largomorphs, and thelike.

The foregoing formulations and administration methods are intended to beillustrative and not limiting. It will be appreciated that, using theteaching provided herein, other suitable formulations and modes ofadministration can be readily devised.

Health Care Product Formulations.

In certain embodiments, one or more of the antimicrobial peptides (AMPs)and/or compound AMPs of the present invention are incorporated intohealthcare formulations, e.g., a prescription or over the counterproduct for use in a home, for travel, at work, in a dental office, at ahospital, etc. Such formulations include, but are not limited totoothpaste, mouthwash, tooth whitening strips or solutions, contact lensstorage, wetting, or cleaning solutions, dental floss, toothpicks,toothbrush bristles, oral sprays, oral lozenges, nasal sprays,aerosolizers for oral and/or nasal application, wound dressings (e.g.,bandages), and the like.

The formulation of such health products is well known to those of skill,and the AMPs and/or compound AMPs of the present invention are simplyadded to such formulations in an effective dose (e.g., a prophylacticdose to inhibit dental carie formation, etc.).

For example, toothpaste formulations are well known to those of skill inthe art. Typically such formulations are mixtures of abrasives andsurfactants; anticaries agents, such as fluoride; tartar controlingredients, such as tetrasodium pyrophosphate and methyl vinylether/maleic anhydride copolymer; pH buffers; humectants, to preventdry-out and increase the pleasant mouth feel; and binders, to provideconsistency and shape (see, e.g., Table 4). Binders keep the solid phaseproperly suspended in the liquid phase to prevent separation of theliquid phase out of the toothpaste. They also provide body to thedentifrice, especially after extrusion from the tube onto thetoothbrush.

TABLE 4 Typical components of toothpaste. Ingredients Wt % Humectants40-70 Water  0-50 Buffers/salts/tartar 0.5-10  control Organicthickeners 0.4-2   (gums) Inorganic thickeners  0-12 Abrasives 10-50Actives (e.g., triclosan) 0.2-1.5 Surfactants 0.5-2   Flavor andsweetener 0.8-1.5 Fluoride sources provide 1000-15000 ppm fluorine.

Table 5 lists typical ingredients used in formulations; the finalcombination will depend on factors such as ingredient compatibility andcost, local customs, and desired benefits and quality to be delivered inthe product. It will be recognized that one or more AMPs and/or compoundAMPs of the present invention can simply be added to such formulationsor used in place of one or more of the other ingredients.

TABLE 5 List of typical ingredients Tartar Inorganic Control GumsThickeners Abrasives Surfactants Humectants Ingredient Sodium SilicaHydrated Sodium Glycerine Tetrasodium carboxymethyl thickeners silicalauryl sulfate pyrophosphate cellulose Cellulose ethers Sodium DicalciumSodium N- Sorbitol Gantrez S-70 aluminum phosphate lauryl silicatesdigydrate sarcosinate Xanthan Gum Clays Calcium Pluronics PropyleneSodium tri- carbonate glycol polyphosphate Carrageenans Sodium Xylitolbicarbonate Sodium alginate Calcium Sodium Polyethylene pyrophosphatelauryl glycol sulfoacetate Carbopols Alumina

One illustrative formulation described in U.S. Pat. No. 6,113,887comprises (1) a water-soluble bactericide selected from the groupconsisting of pyridinium compounds, quaternary ammonium compounds andbiguanide compounds in an amount of 0.001% to 5.0% by weight, based onthe total weight of the composition; (2) a cationically-modifiedhydroxyethylcellulose having an average molecular weight of 1,000,000 orhigher in the hydroxyethylcellulose portion thereof and having acationization degree of 0.05 to 0.5 mol/glucose in an amount of 0.5% to5.0% by weight, based on the total weight of the composition; (3) asurfactant selected from the group consisting of polyoxyethylenepolyoxypropylene block copolymers and alkylolamide compounds in anamount of 0.5% to 13% by weight, based on the total weight of thecomposition; and (4) a polishing agent of the non-silica type in anamount of 5% to 50% by weight, based on the total weight of thecomposition. In certain embodiments, the AMPs and/or compound AMPs ofthis invention can be used in place of the bactericide or in combinationwith the bactericide.

Similarly, mouthwash formulations are also well known to those of skillin the art. Thus, for example, mouthwashes containing sodium fluorideare disclosed in U.S. Pat. Nos. 2,913,373, 3,975,514, and 4,548,809, andin US Patent Publications US 2003/0124068 A1, US 2007/0154410 A1, andthe like. Mouthwashes containing various alkali metal compounds are alsoknown: sodium benzoate (WO 9409752); alkali metal hypohalite (US20020114851A1); chlorine dioxide (CN 1222345); alkali metal phosphate(US 2001/0002252 A1, US 2003/0007937 A1); hydrogen sulfate/carbonate (JP8113519); cetylpyridium chloride (CPC) (see, e.g., U.S. Pat. No.6,117,417, U.S. Pat. No. 5,948,390, and JP 2004051511). Mouthwashescontaining higher alcohol (see, e.g., US 2002/0064505 A1, US2003/0175216 A1); hydrogen peroxide (see, e.g., CN 1385145); CO₂ gasbubbles (see, e.g., JP 1275521 and JP 2157215) are also known. Incertain embodiments, these and other mouthwash formulations can furthercomprise one or more of the AMPs or compound AMPs of this invention.

Contact lens storage, wetting, or cleaning solutions, dental floss,toothpicks, toothbrush bristles, oral sprays, oral lozenges, nasalsprays, and aerosolizers for oral and/or nasal application, and the likeare also well known to those of skill in the art and can readily beadapted to incorporate one or more AMPs and/or compound AMPs of thepresent invention.

The foregoing home healthcare formulations and/or devices are meant tobe illustrative and not limiting. Using teaching provided herein, theAMPs and/or compound AMPs of the present invention can readily beincorporated into other products.

IV. Kits.

In another embodiment this invention provides kits for the inhibition ofan infection and/or for the treatment and/or prevention of dental cariesin a mammal. The kits typically comprise a container containing one ormore of the active agents (i.e., antimicrobial peptides or compoundantimicrobial peptides) described herein. In certain embodiments theactive agent(s) can be provided in a unit dosage formulation (e.g.,suppository, tablet, caplet, patch, etc.) and/or may be optionallycombined with one or more pharmaceutically acceptable excipients.

In certain embodiments the kits comprise one or more of the healthcareproduct formulations described herein (e.g., toothpaste, mouthwash,tooth whitening strips or solutions, contact lens storage, wetting, orcleaning solutions, dental floss, toothpicks, toothbrush bristles, oralsprays, oral lozenges, nasal sprays, aerosolizers for oral and/or nasalapplication, and the like).

In addition, the kits optionally include labeling and/or instructionalmaterials providing directions (i.e., protocols) for the practice of themethods or use of the “therapeutics” or “prophylactics” of thisinvention. Preferred instructional materials describe the use of one ormore active agent(s) of this invention to therapeutically orprophylactically to inhibit or prevent infection and/or to inhibit theformation of dental caries. The instructional materials may also,optionally, teach preferred dosages/therapeutic regiment, counterindications and the like.

While the instructional materials typically comprise written or printedmaterials they are not limited to such. Any medium capable of storingsuch instructions and communicating them to an end user is contemplatedby this invention. Such media include, but are not limited to electronicstorage media (e.g., magnetic discs, tapes, cartridges, chips), opticalmedia (e.g., CD ROM), and the like. Such media may include addresses tointernet sites that provide such instructional materials.

EXAMPLES

The following examples are offered to illustrate, but not to limit theclaimed invention.

Example 1 Novel Synthetic Antimicrobial Peptides Against Streptococcusmutans

Streptococcus mutans, a common oral pathogen and the causative agent ofdental caries, has persisted and even thrived on the tooth surfacedespite constant removal and eradication efforts. In this study, wegenerated a number of synthetic antimicrobial peptides against thisbacterium via construction and screening of several structurally diversepeptide libraries where the hydrophobicity and charge within eachlibrary was varied incrementally in order to generate a collection ofpeptides with different biochemical characteristics. From theselibraries, we identified multiple peptides with robust killing activityagainst S. mutans. To further improve their effectiveness, the mostbactericidal peptides from each library were synthesized together as onemolecule, in various combinations, with and without a flexible peptidelinker between each antimicrobial region. Many of these “fusion”peptides had enhanced killing activities in comparison with those of theoriginal nonconjoined molecules. The results presented here illustratethat small libraries of biochemically constrained peptides can be usedto generate antimicrobial peptides against S. mutans, several of whichcan be functional anticaries agents.

Materials and Methods

Bacterial Strains

S. mutans clinical isolates UA140 (32), UA159 (1), T8 (33), ATCC 25175,GS5 (Kuramitsu and Ingersoll (1977) Infect Immun., 17: 330-337), and allgram-positive strains listed below (see Table 9) were grown underanaerobic conditions in brain heart infusion or Todd-Hewitt (TH) broth(Difco) overnight at 37° C. prior to use (Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 3651-3657). Veillonella atypica PK1910was grown in Veillonella medium (Egland et al. (2004) Proc. Natl. Acad.Sci., USA, 101: 16917-16922). All strains were grown in an anaerobicatmosphere of 80% N₂, 10% CO₂, and 10% H₂.

Peptide Syntheses and Purification.

Peptides were synthesized using 9-fluorenylmethoxyl carbonyl (Fmoc)solid-phase methods on an Apex 396 peptide synthesizer (AAPPTec,Louisville, Ky.). All amino acids, appropriately substituted resins(Anaspec), and reagents (Fisher) were purchased at peptide synthesisgrade. The general synthesis of linear peptides involved the followingprocedure: 0.6 ml of 25% piperidine in dimethylformamide (DMF) was addedto the resin that had been loaded with the first amino acid, followed byagitation for 27 min and wash cycles of dichloromethane (one wash with 1ml), and N-methylpyrrolidone (seven washes with 0.8 ml each time). Forcoupling, a 5 M excess of Fmoc-protected amino acid,N-hydroxybenzotrazole, HBTU(O-benzotriazole-N,N,N′,N′-tetramethyl-uronium-hexafluoro-phosphate),and diisopropyl ethyl-amine (10 M excess) in DMF (0.1 ml) andN-methylpyrrolidone (0.2 ml) was added, and the reaction mixture wasagitated for 45 min. Following the coupling of the last amino acid tothe resin, the protected peptide was cleaved from the resin with 1 ml oftrifluoroacetic acid-thioanisole-water-1,2-ethanedithiol (10 ml:0.5ml:0.5 ml:0.25 ml) for 2 h at room temperature and washed sequentiallywith DMF, methanol, and dichloromethane and dried overnight undervacuum.

Analytical and preparative reverse-phase high-performance liquidchromatographies (ACTA purifier; Amersham) was conducted with a Source15RPC column eluted with H₂O and CH₃CN with 0.1% trifluoroacetic acid ina linear gradient as described previously (Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 3833-3838). All peptides were purifiedto >90% (data not shown). Peptide mass was confirmed by matrix-assistedlaser desorption ionization-mass spectrometry and conducted with samplesdissolved in a 1:2 mixture of H₂O—CH₃CN. Measurements were made in thelinear mode, with an α-cyano-4-hydroxycinnamic acid matrix (Voyagersystem; ABI). The mass observed corresponded in all cases with thecalculated value (data not shown).

Estimation of Peptide Characteristics.

Peptide average hydrophobicity per residue (<H>) was calculated usingthe scale of Fauchere and Pliska (Fauchere and Pliska (1983) Eur. J.Med. Chem. 18: 369-375), available at//us.expasy.org/tools/pscale/Hphob.Fauchere.html. This method wasselected for calculating the hydrophobicity of AMPs due to its agreementwith experimental evidence describing the membrane affinity ofindividual amino acids in a host-guest system (Thorgeirsson et al.(1996) Biochemistry 35: 1803-1809). The average a-helix-formingpropensity per residue (<Helix>) was estimated utilizing the scaledeveloped by Liu and Deber that defines the helical propensities ofindividual amino acids in nonpolar membrane environments, such as thoseencountered by AMPs at the surface of the target cell (Lehrer and Ganz(2002) Curr. Opin. Immunol. 14: 96-102).

MIC Assays.

Antibacterial growth inhibition assays were performed using sterile96-well plates in a final volume of 100 μl, TH or Veillonella medium asdescribed previously (Qi et al. (2005) FEMS Microbial Lett. 251:321-326). Briefly, bacterial cells were grown overnight to an opticaldensity at 600 nm of 0.75 to 0.8 (corresponding to 1×10⁸ CFU/ml) andthen diluted to 1×10⁵ CFU/ml in broth and aliquoted onto plates. Anappropriate volume of peptide stock solution (5 to 20 mg/ml, in water ormethanol, depending on solubility) was then added to the first column ofthe plate to give 500 μg/ml or 512 μg/ml, followed by serial 1:2dilutions across the plate to give wells containing peptides rangingfrom 500 to 1.95 μg/ml or 512 to 2 μg/ml. Methanol alone was also addedto control for the effects of the solvent. The plates were thenincubated at 37° C. under anaerobic conditions for 16 to 20 h withoutshaking, and the MIC was determined as the concentration of peptidepresent in the last clear well after visual inspection. Up to 5%(vol/vol) methanol was found not to be antimicrobial (data not shown).MICs were determined in triplicate for all bacteria.

Assessment of Antimicrobial Kinetics.

The determination of killing kinetics for fusion and parental peptideswas conducted essentially as described previously (Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 1480-1488). Briefly, medium-dilutedovernight UA159 cultures (0.5×10⁶ to 1×10⁶ CFU/ml) were challenged withpeptide at a concentration of 25 μg/ml, and at the indicated timeintervals (“0 min” indicates untreated samples), a 10-μL aliquot wasremoved and the surviving CFU were rescued by dilution (1:50) intogrowth medium and then spread on TH agar plates for quantitation. Whereinitial experiments suggested few survivors (<3,000 CFU/ml), entire 1-mlsamples were plated without aliquots. Kinetics were determined byrecording the average number of surviving CFU/ml versus incubation timein the presence of peptide (all assays were independently repeated threeto five times). For Table 8, time to bactericidal killing (TC) valueswere defined as the time required for the level of surviving CFU/ml frompeptide-treated cultures to fall 3 log₁₀ below the levels of recoveredS. mutans CFU/ml from untreated samples.

Results.

Design of Constrained Peptide Libraries.

We hypothesized that a series of small peptide libraries which containedgradients of incrementally varied hydrophobic and cationic character,within constrained predicted conformational frameworks, would containAMPs with activity against S. mutans. Three libraries were developed forthis study: the binary, a-helix, and RW libraries. Peptides within thebinary and a-helix libraries were designed from an amphipathic,a-helical sequence arrangement framework (HCCHHCHHCC_(n) (SEQ ID NO:30),where His a hydrophobic residue and C is a charged residue) that wasdeveloped from several published AMP amphipathic sequence templates(Blondelle and Lohner (2000) Biopolymers 55: 74-87; Zelezetsky et al.(2005) Peptides 26: 2368-2376) and was validated using helical-wheelprojections (Schiffer and Edmundson (1967) Biophys J., 7: 121-135) andthe average helical propensity <Helix> (Table 6). FIG. 1 shows tworepresentative projections from each library. The lengths of thepeptides within the binary and a-helix libraries were limited to 11 and14 amino acids, respectively, near the estimated number of minimalresidues required to form membrane-spanning pores (Shai (2002)Biopolymers 66: 236-248). From within this structural framework, thebinary library was constructed by reducing, in a stepwise manner, thehydrophobic/aromatic and cationic components within a baseline sequence,FKKFWKW FRRF (B-33, SEQ ID NO:31), via the substitution ofless-hydrophobic/aromatic or positively charged residues (B-33 has beenpublished with alternative nomenclature, S6L3-33 [Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 3651-3657]). The resulting gradient ofcharge and hydrophobicity (<H>) within this library of 32 peptides isshown in Table 6. The α-helix library was designed to be longer than thebinary library (14 versus 11 amino acids), and in a manner similar tothat of the binary library, the hydrophobicity and charge were variedincrementally throughout the a-helix library (Table 6).

TABLE 6Sequences and antimicrobial activities of binary, alpha-helix, andRW library peptides against clinical isolates of S. mutans. Sequence^(a)MIC^(b) Net Peptide (SEQ ID NO) (μg/ml) charge^(c) <H> <Helix>Binary library B-33 FKKFWKWFRRF* 8-24 +6 0.61 0.71 (SEQ ID NO: 31) B-34LKRFLKWFKRF* 8-24 +6 0.55 0.94 (SEQ ID NO: 32) B-35 KLFKRWKHLFR31.25-125  +5 0.18 0.85 (SEQ ID NO: 33) B-36 RLLKRFKHLFK 31.25-125  +50.35 1.05 (SEQ ID NO: 34) B-37 FKTFLKWLHRF* 24 +4 0.77 1.06(SEQ ID NO: 35) B-38 IKQLLHFFQRF* 24 +3 0.75 1.21 (SEQ ID NO: 36) B-39KLLQTFKQIFR >250 +3 0.50 1.11 (SEQ ID NO: 37) B-40 RILKELKNLFK >250 +30.32 1.23 (SEQ ID NO: 38) B-41 LKQFVHFIHRF* 32 +3 0.74 1.20(SEQ ID NO: 39) B-42 VKTLLHIFQRF* 31.25-125  +3 0.56 1.32(SEQ ID NO: 40) B-43 KLVEQLKEIFR >250 +1 0.16 1.10 (SEQ ID NO: 41) B-44RVLQEIKQILK >250 +2 0.43 1.21 (SEQ ID NO: 42) B-45 VKNLAELVHRF* >250 +20.35 1.25 (SEQ ID NO: 43) B-46 ATHLLHALQRF* >250 +2 0.62 1.31(SEQ ID NO: 44) B-47 KLAENVKEILR >250 +1 0.25 1.12 (SEQ ID NO: 45) B-48RALHEAKEALK >250 +1 0.02 1.02 (SEQ ID NO: 46) B-49 FHYFWHWFHRF* 125 +21.09 0.79 (SEQ ID NO: 47) B-50 LYHFLHWFQRF* 125 +2 1.00 1.05(SEQ ID NO: 48) B-51 YLFQTWQHLFR >125 +1 0.83 0.95 (SEQ ID NO: 49) B-52YLLTEFQHLFK >125 0 0.74 1.13 (SEQ ID NO: 50) B-53 FKTFLQWLHRF* 16-64 +30.84 1.06 (SEQ ID NO: 51) B-54 IKTLLHFFQRF* 32-62.5 +3 0.79 1.26(SEQ ID NO: 52) B-55 KLLQTFNQIFR >125 +2 0.54 1.10 (SEQ ID NO: 53) B-56TILQSLICNIFK >125 +2 0.56 1.24 (SEQ ID NO: 54) B-57 LKQFVKFIHRF* 24 +40.64 1.18 (SEQ ID NO: 55) B-58 VKQLLKIFNRF* 32-62.5 +4 0.56 1.25(SEQ ID NO: 56) B-59 KLVQQLKNIFR >125 +3 0.38 1.11 (SEQ ID NO: 57) B-60RVLNQVKQILK >125 +3 0.33 1.17 (SEQ ID NO: 58) B-61 VKKLAKLVRRF* 16-32 +60.27 1.21 (SEQ ID NO: 59) B-62 AKRLLKVLKRF* 16-32 +6 0.31 1.25(SEQ ID NO: 60) B-63 KLAQKVKRVLR >125 +5 0.18 1.10 (SEQ ID NO: 61) B-64RALKRIKHVLK >125 +5 0.06 1.15 (SEQ ID NO: 62) Alpha helix library α-4AQAAHQAAHAAHQF* >125 +1 0.26 1.13 (SEQ ID NO: 63) α-5 KLKKLLKKLKKLLK 8+8 0.16 1.13 (SEQ ID NO: 64) α-6 LKLLICKLLKLLKKF* 8 +7 0.55 1.42(SEQ ID NO: 65) α-7 LQLLKQLLKLLKQF* 8 +4 0.72 1.42 (SEQ ID NO: 66) α-8AQAAKQAAKAAKQF* >125 +4 0.026  1.09 (SEQ ID NO: 67) α-9 RWRRWWRHFHHFFH*8 +5 0.61 0.55 (SEQ ID NO: 68) α-10 KLKKLLKRWRRWWR 8 +8 0.28 0.68(SEQ ID NO: 69) α-11 RWRRLLKKLHHLLH* 8 +6 0.44 1.02 (SEQ ID NO: 70) α-12KLKKLLKHLHHLLH* 8 +5 0.48 1.18 (SEQ ID NO: 71) RW library 1C-1 RRRRWWW16 +4 0.39 0.24 (SEQ ID NO: 72) 1C-2 RRWWRRW 16 +4 0.39 0.24(SEQ ID NO: 73) 1C-3 RRRWWWR 32 +4 0.39 0.24 (SEQ ID NO: 74) 1C-4RWRWRWR 32 +4 0.39 0.24 (SEQ ID NO: 75) 2C-1 RRRFWWR 31.25-125  +4 0.320.41 (SEQ ID NO: 76) 2C-2 RRWWRRF* 12-24 +5 0.32 0.41 (SEQ ID NO: 77)2C-3 RRRWWWF* 4-8 +4 0.79 0.46 (SEQ ID NO: 78) 2C-4 RWRWRWF* 4-8 +4 0.790.46 (SEQ ID NO: 79) 3C-1 RRRRWWK 125 +5 −0.076 0.19 (SEQ ID NO: 80)3C-2 RRWWRRK 125 +5 −0.076 0.19 (SEQ ID NO: 81) 3C-3 RRRWWWK 31.25-125 +4 0.39 0.24 (SEQ ID NO: 82) 3C-4 RWRWRWK 32 +4 0.39 0.24(SEQ ID NO: 83) 4C-1 RRRKWWK 250 +5 −0.073 0.19 (SEQ ID NO: 84) 4C-2RRWKRRK 500 +6 −0.39  0.13 (SEQ ID NO: 85) 4C-3 RRRKWWK 125 +5 −0.51 0.19 (SEQ ID NO: 86) 4C-4 RWRKRWK 125-500 +5 −0.51  0.19 (SEQ ID NO: 87)^(a)An asterisk indicates an amidated C. terminus. ^(b)MIC range orvalue from all S. mutans isolates tested. ^(c)Charge at pH 7.0,calculated as described previously (Zhang et al. (2001) J. Biol. Chem.,276: 35714-35722).

Many naturally occurring AMPs contain numerous Arg and Trp residues(Chan et al. (2007) Biochim Biophys Acta. 51(4): 1351-1359), andprevious reports have shown that a predominance of these amino acidsappear in hexameric AMPs generated via synthetic combinatorial, orsimilar, methods (Blondelle and Houghten (1996) Trends Biotechnol., 14:60-65; Chan et al. (2007) Biochim Biophys Acta. 51(4): 1351-1359).Therefore, we constructed the RW library to contain Arg- and Trp-rich (Rand W) heptamers that were varied in order of basic (Arg or Lys) and Trpresidues and in ratio of basic to hydrophobic residues, as shown inTable 6. These sequences were not designed to form conventional α-helixconformations, as reflected in their low <Helix> values.

Activity of Binary Library Peptides.

The binary library was evaluated for S. mutans activity against acollection of clinical isolates by an MIC assay (Table 6). Two peptidesthat showed the lowest MICs (range, 8 to 24 μg/ml), B-33 and B-34, werealso the most hydrophobic and cationic in the binary library. Similarly,B-37, -38, -41, -53, -54, -57, and -58, peptides that were active but toa lesser degree than B-33 or B-34, possessed net charges of at least +3and an <H> of >0.55. In contrast, peptides with hydrophobicity valuesbelow 0.55 were not antimicrobial, with two exceptions: B-61 and B-62(MIC range, 16 to 32 μg/ml). Notably, these two peptides each had onlyone aromatic residue but a net charge of +6 that may contribute to theirsustained activity.

The MIC results are consistent with the idea that net positive chargeand some hydrophobic content are critical parameters for designingactive peptides (Chan et al. (2007) Biochim Biophys Acta. 51(4):1351-1359; Deslouches et al. (2005) Antimicrob. Agents Chemother. 49:316-322). Accordingly, the addition of negatively charged residues,especially to the central area of the peptide, appears to abolish AMPactivity (for example, B-43), likely due to the interruption of thepositive charge necessary for peptide attraction to the bacterialsurface. The data indicate two interesting exceptions, B-49 and B-50,which are weakly active despite the lack of strong cationic character.The exceptionally high <H> values (and therefore likely rapid partitioninto host membranes) for these peptides may explain this discrepancy.B-33, -34, and -38, three of the more active peptides from this library,were selected for further enhancement. Interestingly, as was the casethroughout this study, no strain of S. mutans appeared more susceptibleor resistant to the AMPS tested (data not shown)

Activity of the Alpha-Helix Library Peptides.

As shown in Table 6, many of the a-helix library peptides had robustactivities against S. mutans, as evaluated by MIC: only two peptideswith low net positive charges or <H> values (α-4 and α-8, respectively)were inactive. Though many a-helix library peptides showed equallyrobust killing activities against S. mutans, α-11 alone was selected forfurther modification.

Activity of RW Library Peptides.

As shown in Table 6, we observed that 2C-3 and 2C-4 were the most activepeptides against S. mutans (MIC range, 4 to 8 μg/ml) from the RW (Arg-and Trp-rich) library. These data indicate that a near 1:1 ratio ofhydrophobic to charged amino acids (including the amidated C-terminalPhe as a charged residue) is required for robust antimicrobial activity,similar to the reported ratio of 4:3 observed by Blondelle and othersexamining Trp/Arg-rich AMPs (Blondelle et al. (1996) Antimicrob. AgentsChemother. 40: 1067-1071; Shai (2002) Biopolymers 66: 236-248). RWlibrary peptides with a lower ratio of hydrophobic to charged aminoacids (reflected in lower <H> values) were not as active as 2C-3 or2C-4. Due to their low MICs, these peptides were selected for furtherenhancement.

Design of Fusion AMPs.

Previous studies have shown that synthesizing AMPs as conjoined lineardimers or pentameric bundles, in various arrangements, can increasepeptide activity compared to that of the single constituent AMP alone(Devi et al. (1998) J. Biomol. Struct. Dyn. 15: 653-651; Sal-Man et al.(2002) Biochemistry 41: 11921-11930). In a similar manner, wehypothesized that the activity of the S. mutans-active sequences shownin Table 6 could be improved by synthesizing two AMPs together, head totail, as a single fusion linear peptide molecule. It was noted in ourprevious studies that a linker region between peptide domains has animpact on antimicrobial activity (Eckert et al. (2006) Antimicrob.Agents Chemother. 50: 1480-1488). Therefore, in the hopes of generatingpeptides with greater activity against S. mutans, we synthesized alibrary of fusion peptides (Table 7) that differed in the arrangement ofconstituent AMPs and the sequence of linker regions (or with no linker)between each.

In the binary-to-alpha-helix set, B-33 and B-38 were synthesized withα-11 at the N or C terminus. A tri-Gly linker, which has been shownpreviously to be effective in separating functionally independentpeptide regions within a linear sequence (Eckert et al. (2006)Antimicrob. Agents Chemother. 50: 1480-1488) and may be critical forpeptide secondary-structure transition in model membranes (Tack et al.(2002) Eur. J. Biochem. 269: 1181-1189), was employed to separate thetwo AMP domains. The RW-to-RW set of fusion peptides contained 2C-3 and2C-4 as linear homodimers with or without various linker regions inbetween. In the last group shown in Table 7 (binary-to-RW set), 2C-4 wassynthesized with B-33, -34, or -38 at the N or C terminus, againseparated by a Gly linker region. These arrangements allowed us toinvestigate the importance of linker composition (and presence) as wellas AMP subunit arrangement (N or C terminus within the fusion peptide)on anti-S. mutans activity.

Antimicrobial Activity of Fusion AMPs.

MICs revealed that fusion AMPs were largely equally or less active thantheir parent AMPs against S. mutans (Table 7). Exceptions includedFBα-20, which had a reduced MIC range compared to either B-33 or α-11,and FBRW-22, which had a slightly reduced MIC range compared with theparent peptide B-33. Overall, these data indicate that fusing AMPsresults, at best, in only modest improvements in MIC. However, MICassays can obscure dramatic differences in killing speed betweencomparable peptides (Eckert et al. (2006) Antimicrob. Agents Chemother.50: 1480-1488), suggesting that a more detailed analysis of peptidekilling kinetics was necessary to fully evaluate fusion AMPs.

TABLE 7 Sequence and activity of fusion library peptides SEQ ID PeptideSequence^(a) (μg/ml)^(b)  NO Binary-to-a-helical linker FBα-12FKKFWKWFRRF-GGG- 16 88 RWRRLLKKLHHLLH* FBα-13 IKQLLHFFQRF-GGG- 16 89RWRRLLKKLHHLLH* FBα-20 RWRRLLKKLHHLLH- 4-8 90 GGG-FKKFWKWFRRF* FBα-21RWRRLLKKLHHLLH- 16 91 GGG-IKQLLHFFQRF* RW-to-RW linker FRW-2RRRWVVWFRRRWWWF* 16 92 FRW-8 RWRWRWFRWRWRWF* 16 93 FRW-3 RRRWWWF-ASASA-32 94 RRRWWWF* FRW-4 RRRWWWF-PSGSP- 32 95 RRRWWWF* FRW-5 RRRWWWF-GGG- 1696 RRRWWWF* FRW-9 RWRWRWF-ASASA- 16 97 RWRWRWF* FRW-10 RWRWRWF-PSGSP- 3298 RWRWRWF* FRW-11 RWRWRWF-GGG- 16 99 RWRWRWF* Binary-to-RW linkerFBRW-14 FKKFWKWFRRF-GGG-  4-16 100 RWRWRWF* FBRW-15 IKQLLHFFQRF-GGG- 4-16 101 RWRWRWF* FBRW-16 LKRFLKWFKRF-GGG-  4-16 102 RWRWRWF* FBRW-22RWRWRWF-GGG- 4-8 103 FKKFWKWFRRF* FBRW-23 RWRWRWF-GGG- 8-16 104IKQLLBFFQWRF* FBRW-24 RWRWRWF-GGG- 8 105 LKRFLKWFKRF* ^(a)An asteriskdenotes an amidated C terminus. ^(b)MIC range or value from all S.mutans isolates tested, with a minimum of three independent trials.

The killing kinetics of fusion AMPs against S. mutans were analyzed bytime-kill assays. As shown in FIG. 2A, the fusion peptide FBα-21 had anobvious increase in killing kinetics compared to either B-34 or o-11:more than 2 log₁₀ fewer CFU/ml were recovered from fusionpeptide-treated cultures than from parental peptide-treated samplesafter 30 min. This trend was representative of all the FBα peptides(data not shown).

An increase in killing kinetics for all binary-RW library conjugates(with the exception of FBRW-14 and -23) was also conspicuous (FIG. 2B):fusion peptides with the binary library AMP at the N or C terminusrelative to 2C-4 were equally effective in improving the level of S.mutans killing more than 3 log₁₀ after 30 min of treatment, comparedwith samples treated with either parent peptide. The results indicatethat the conjoined AMP domains may be exerting an enhanced killingeffect against S. mutans that is best observable after short periods ofpeptide exposure.

As shown in Table 8, we also observed an increase in killing kineticsfor some RW-to-RW fusion peptides. In samples treated with the 2C-4homodimer without a linker region (FRW-8), the surviving number of S.mutans CFU/ml dropped 3 log₁₀ below that of untreated samples (definedas time to bactericidal activity, or T_(c)) by 50 min, while 2C-4 had aT_(C) of 220 min. This trend, to a lesser extent, was also present whensamples exposed to the 2C-3 homodimer without a linker (FRW-2) werecompared to samples treated with its parent peptide (2C-3).Interestingly, the addition of a linker region of flexible amino acids(either PSGSP (SEQ ID NO:106), ASASA (SEQ ID NO:107), or GGG (SEQ IDNO:108)) between 2C-3 domains did not result in an improvement inkilling kinetics (T_(C) of >250 min for FRW-3 to −5), while 2C-4homodimers FRW-9 and -11 had increased bactericidal speed relative tothat of the parent 2C-4 AMP despite the presence of ASASA (SEQ IDNO:107) and GGG (SEQ ID NO:108) linker regions, respectively (Table 8).These results suggest that RW-based peptide activity against S. mutanscan be enhanced by synthesizing peptides together without a linkerregion, but when a linker region is utilized, the data indicate thatincreased kinetics are likely sequence and therefore secondary structuredependent, as 2C-4 could be improved by conjugations with linker regionsof flexible amino acids (except PSGSP, SEQ ID NO:106) and 2C-3 couldnot.

TABLE 8 Bactericidal kinetics of parent RW and fusion FRW librarypeptides T_(C) Peptide Linker composition (min)^(a) Parental AMPs 2C-3220 2C-4 230 2C-3 fusions FRW-2 No linker 60 FRW-3 ASASA 480 FRW-4 PSGSP420 FRW-5 GGG 270 2C-4 fusions FRW-8 No linker 50 FRW-9 ASASA 45 FRW-10PSGSP 270 FRW-11 GGG 90 ^(a)T_(C), time required to kill 3 log₁₀ ofrecoverable CFU/ml.

Peptide Activity Against Other Oral Bacteria.

A set of peptides with the best anti-S. mutans activity (as measured byMIC) were selected to investigate the activity of these AMPs againstseveral normally commensal oral streptococcal strains and Lactobacilluscasei, as well as the oral gram-negative organism V. atypica (Table 9).The MIC results indicate that these sequences were active, but to alesser degree than seen with S. mutans, against Streptococcus gordonii,L. casei, and Streptococcus sanguinis. All peptides examined weretypically only weakly active against Streptococcus mitis. V . atypicaappeared more susceptible to α-11 than the other bacteria tested but wasmore resistant to the RW library peptides 2C-3 and 2C-4.

TABLE 9 MICs of selected peptides against non-S. mutans oral isolatesMIC (μg/ml) S. mitis L. casei S. gordonii ATCC S. sanguinis ATCC V.atypica Peptide Challis DL1 903 NY101 4646 PK1910 B-33 32 32 32 32 16B-34 32 64 16 16 32 B-38 32 64 64 32 64 α-11 16 32 16 16 4 2C-3 32 32 1616 64 2C-4 32 32 32 32 64 FBα-20 16 32 16 8 8 FBRW-14 32 64 16 8 8FBRW-15 32 64 16 16 8 FBRW-16 64 64 16 16 8 FBRW-22 16 64 8 8 8 FBRW-2432 64 16 8 16

Discussion

In the United States, the high financial burden associated with treatingdental caries, especially among underprivileged and minority populations(Anderson and Shi (2006) Pediatr. Dent., 28: 151-153; discussion192-198; National Institutes of Health (2000) Oral health in America: areport of the Surgeon General, Department of Health and Human Services,National Institute of Dental and Craniofacial Research, NationalInstitutes of Health, Bethesda, Md.; Washington State Department ofHealth (2002) Infectious Diseases—Dental Caries, Washington StateDepartment of Health, Olympia, Wash.), could be alleviated by dentalhygiene regimens supplemented with more-effective anti-S. mutanstherapeutics. Accordingly, the results presented here suggest thatpeptides with robust activity against S. mutans can be identified byscreening small rationally designed libraries. Interestingly, themost-active peptides derived in this study appear to have some activityagainst other gram-positive oral bacteria, although more data arerequired to fully evaluate whether the hydrophobic and amphipathiccharacteristics of these sequences are indicative of generalanti-gram-positive bacterial activity. As S. mutans normally grows in abiofilm state in vivo, we were encouraged to also find that all thepeptides in Table 9 had activity against in vitro S. mutans biofilmsgrown on glass slides in the presence of sucrose (data not shown).

For the binary and α-helix libraries, the results indicate that maximalS. mutans activity occurred in peptides with both high relativehydrophobicity and more than +3 net positive charge. Intermediate levelsof activity were observed for peptides whose properties were dominatedby either single trait. These results are consistent with what is knownof most synthetic and natural AMPs with cationic amphipathic characterand suggest that B-33, α-7, and the other active peptide sequences inthese libraries may behave in a manner similar to that of other AMPswithin this structural class; i.e., the positive charge of the peptideis thought to be required for the attraction of AMP to anionic bacterialmembranes, while the amphipathicity is necessary for membraneinteraction, helix transition, and cell killing (Jing et al. (2003) J.Pept. Res. 61: 219-229; Shai (2002) Biopolymers 66: 236-248). Theseresults also indicate that a high <Helix> value, on its own, may notcorrelate with increased anti-S. mutans activity for cationicamphipathic AMPs.

For the RW library, as was the case with the binary and α-helixlibraries, the most-hydrophobic and cationic sequences were the mostactive (2C-3 and -4). Despite the differences in length and periodicitycompared with peptides in the other libraries, RW peptides are believedto be capable of gaining enhanced activity from improvements in initialpeptide binding or membrane insertion. This is supported by evidenceindicating that Arg- and Trp-rich peptides, despite their low <Helix>values, form stable helix-like amphipathic arrangements upon membraneinteraction which are stabilized by electrostatic bonds between the TrpH electrons and the Arg functional group (Jing et al. (2003) J. Pept.Res. 61: 219-229; Mecozzi et al. (1996) Proc. Natl. Acad. Sci., USA, 93:10566-10571). Thus, the unique sequence properties of the RW librarypeptides may allow them to obtain secondary structures that are highlyconducive to antimicrobial activity.

Interestingly, our results indicate that fusion peptides, AMP dimerssynthesized as single linear molecules, often have in creased killingkinetics compared to their parental peptides. Some fusion peptides mayfunction by increasing the number of helix-forming units per molecule atthe membrane surface, as has been described for bundled AMPs (Sawai etal. (2002) Protein Eng. 15: 225-232). The data are unclear regarding theimpact of linker regions between AMP segments, though it does appearthat linker regions may affect individual peptides differently (seeresults for FRW-3 and FRW-9 in Tables 7 and 8). Studies are under way todirectly investigate the impact of linker composition on AMP activity.Furthermore, our results suggest that the effect of constituentarrangement (which fusion peptide subunit goes at the C or N terminus)is also difficult to predict (compare the MICs of FBα-12 and FBα-20),though other work has demonstrated that amphipathic and putativehelix-forming AMPs appear to be more tolerant of N-terminal additionsfor reasons that remain unclear (Eckert et al. (2006) Antimicrob. AgentsChemother. 50: 1480-1488; Szynol et al. (2006) Chem. Biol. Drug Des.,67: 425-431).

In conclusion, our results indicate that S. mutans appears to besusceptible to peptides with relatively high hydrophobicity and cationiccharge, which were readily isolated from our constrained libraries.Additionally, fusion peptides constructed from conjoining activesequences from within and between these libraries improved the killingkinetics of these peptides.

Example 2 Activity of Acid-Activated Library Peptides

Histidine residues have a side-chain pKa near 6.0, and therefore carry acationic charge at pH 6.0 and below, but not at neutral pH. Weconstructed the Acid-activated Library with this characteristic in mind,so that an amphipathic, helix forming arrangement (leading to anti-S.mutans activity) would result in a low pH environment (such as thatcreated by S. mutans on a carious lesion), but the peptides would remaininactive above pH 6.0. Validating this hypothesis, the majority of thesequences in this library were found to have strong antimicrobialactivity against S. mutans at pH 4.9, but were inactive at pH 7.4 (Table10). Peptides from this library were not selected for furtherenhancement during this study.

TABLE 10 MIC of acid-activated library peptides against S. mutans.MIC(μM) Peptide Sequence SEQ ID NO pH 7.4 pH 4.9 AA-1 HHFFHHFHHFFHHF*109 >125 12.5 AA-2 HHFFHHFFHFFHHF* 110 >125 3.125 AA-3KLLKGATFHFFHHFFHFFHHF 111 >125 6.25 AA-4 KLKFHFFHHFFHFFHHF 112 >1253.125 AA-5 FHFFHHFFHFFHHFKLLK 113 >125 28.125 AA-6 FHYFWHWFHRF 114125 >50 AA-7 LYHFLHWFQRF 115 125 >50 * denotes amidated C-terminus

Example 3 Activity of Killing Peptide Library #7

Peptides within Killing Library #7 (Table 11), were designed to besmall, hydrophobic, and to have weak cationic character relative to theother libraries described herein. MIC studies against S. mutans revealedthat many of the sequences within this library were non-active or weaklyactive. S6L1-5 showed moderate activity. No peptides from within thislibrary were selected for further study.

TABLE 11 Killing Peptide Library #7. MIC(μg/mL) Peptide SequenceSEQ ID NO S. mutans S. aureus P. aeruginosa S6L1-2 LKQKLK1LF* 116125 >500 >500 S6L1-3 LKQLKAGIY* 117 >500 >500 250 S6L1-4 VGKCVKLLY* 118125 500 250 S6L1-5 KFVKLI LAY* 119 32 >500 92 S6L1-6 KLVKLVFLY* 120125 >500 >500 S6L1-7 IKVFAKQKY* 121 >500 >500 >500 S6L1-8 RFRHFQERY* 12264 125 >500 * denotes amidated C-terminus

Example 4 Activity of Beta-Deletion Library Peptides

The hydrophobic and cationic peptides found within this library weresystematically shortened from 15 amino acids to 7, to give a gradient ofphysical size while holding the hydrophobicity and charge parametersgenerally stable. We observed that several of the sequences within thislibrary had robust anti-S. mutans activity as evaluated by MIC (Table12). The active sequences included peptides of varying sizes, though ourdata indicate that at least 9 residues are required for activity. Wealso found that peptides in this library were not generally activeagainst the Gram-negative organism examined, Pseudomonas aeruginosa, buthad activity against several other Gram-positive bacteria. Thesepeptides were not selected for further enhancement during this study.

TABLE 12 Beta-deletion library. MIC (μg/mL) Peptide Sequence E. faecalisL. casei S. aureus P. aeruginosa S. mutans S3L8-1 FVFRHKWVWKHRFLF 3262.5 >125 >125 16 (SEQ ID NO: 123) S3L8-2VFIVWVHKHVLF >125 >62.5 >125 >125 N/A (SEQ ID NO: 124) S3L8-3WRWRARWRWRLRWRF 8 16 16 >125 4 (SEQ ID NO: 125) S3L8-4 WRIHLRARLHVKFRF 88 62.5 >125 N/A (SEQ ID NO: 126) S3L8-5 LRIHARFKVHIRLKF 12 8 >125 >12560 (SEQ ID NO: 127) S3L8-6 FHIKFRVHLKVRFHF >125 8 >125 >125 N/A(SEQ ID NO: 128) S3L8-7 FHVKIHFRLHVKFHF >125 16 >125 >125 N/A(SEQ ID NO: 129) S3L8-8 LHIHAHFHVHIHLHF >125 >62.5 >125 >125 N/A(SEQ ID NO: 130) S3L8-9 FKIHFRLKVHIRFICF >125 8 >125 >125 N/A(SEQ ID NO: 131) S3L8-10 FKAHIRFKLRVKFHF >125 8 >125 >125 N/A(SEQ ID NO: 132) S3L8-11 LKAKIKFKVKLKIKF 39 3 125 32-62.5 8(SEQ ID NO: 133) S3L8-12 WIWKHKFLHRHFLF 125 >62.5 >125 >125 125(SEQ ID NO: 134) S3L8-13 VFLHRHVIKHKLVF 125 >62.5 >125 >125 N/A(SEQ ID NO: 135) S3L8-14 FLHKHVLRHRIVF >125 >62.5 >125 >125 N/A(SEQ ID NO: 136) S3L8-15 VFKHKWHRHILF 125 >62.5 >125 >125 31(SEQ ID NO: 137) S3L8-16 FLFKHLFLHRIFF >125 >62.5 >125 >125 >125(SEQ ID NO: 138) S3L8-17 LFKHILHIRVIF 125 >62.5 >125 >125 >125(SEQ ID NO: 139) S3L8-18 FLHKHLFKHKLF >125 >62.5 >125 >125 >125(SEQ ID NO: 140) S3L8-19 VFRHRFIHRHVF >125 >62.5 >125 >125 >125(SEQ ID NO: 141) S3L8-20 FIHKLVIIKHVLF >125 >62.5 >125 >125 >125(SEQ ID NO: 142) S3L8-21 VLRHLFRHRIVF 93.5 >62.5 >125 >125 60(SEQ ID NO: 143) S3L8-22 LVHKLILRHLLF >125 >62.5 >125 >125 >125(SEQ ID NO: 144) S3L8-23 VFKRVLIHKLIF 32 62.5 >125 >125 >125(SEQ ID NO: 145) S3L8-24 VRKFLFRHKVF 32 62.5 >125 >125 >125(SEQ ID NO: 146) S3L8-25 VLKHVIAHKRLF >125 >62.5 >125 >125 >125(SEQ ID NO: 147) S3L8-26 FIRKFLFKHLF 24 16 62.5 >125 16 (SEQIDNO:148)S3L8-27 VIRHVWVRKLF >125 >62.5 >125 >125 60 (SEQ ID NO: 149) S3L8-28FLFRHRFRHRLVF 62.5 >62.5 >125 >125 60 (SEQ ED NO: 150) S3L8-29.FLHKHAKHKFLF >125 >62.5 >125 >125 >125 (SEQIDNO:151) S3L8-30FKHKFKHKFIF >125 >62.5 >125 >125 >125 (SEQ ID NO: 152) S3L8-31LRHRLRHRLIF 125 >62.5 >125 >125 >125 (SEQ ID NO: 153) S3L8-32LILKFLFKFVF 16 16 16 >125 31 (SEQ ID NO: 154) S3L8-33 VLIRILVRVIF 16 16125 >125 >125 (SEQ ID NO: 155) S3L8-34FRHRFRHRF >125 >62.5 >125 >125 >125 (SEQ ID NO: 156) S3L8-35LKHKLKHKF >125 >62.5 >125 >125 >125 (SEQ ID NO: 157) S3L8-36FKFKHKLIF >125 >62.5 >125 >125 >125 (SEQ ID NO: 158) S3L8-37LRLRHRVLF >125 >62.5 >125 >125 >125 (SEQ ID NO: 159) S3L8-38FKFLFKFLF >125 32 >125 >125 >125 (SEQ ID NO: 160) S3L8-39 LRLFLRWLF 3216 16 >125 16 (SEQ ID NO: 161) S3L8-40 FKFLFKHKF 62.5 62.5 >125 >125 30(SEQ ID NO: 162) S3L8-41 LRLFLRHRF 62.5 >62.5 >125 >125 16(SEQ ID NO: 163) S3L8-42 FKFLFKF >125 >62.5 >125 >125 >125(SEQ ID NO: 164) S3L8-43 LRLFLRF >125 >62.5 >125 >125 >125(SEQ ID NO: 165)

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

1. An antimicrobial peptide said peptide comprising the following aminoacid motif or a circular permutation of the following amino acid motif:(H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵)_(n) wherein: n ranges from 1 to 5 and canincrement by units of 0.1; H¹, H², H³, H⁴, and H⁵ are independentlyselected hydrophobic or hydrophilic amino acids; C¹, C², C³, C⁴, and C⁵are independently selected uncharged amino acids, positively chargedamino acids, or negatively charged amino acids; said peptide forms analpha helix; and said peptide is effective to kill or inhibit the growthor proliferation of Streptococcus mutans in culture. 2: Theantimicrobial peptide of claim 1, wherein said peptide excludes theamino acid sequence FKKFWKW FRRF (SEQ ID NO:31); 3: The antimicrobialpeptide of claim 1, wherein C¹, C², C³, C⁴, and C⁵ are independentlyselected positively charged amino acids, or negatively charged aminoacids. 4-7. (canceled)
 8. The antimicrobial peptide of claim 1, wherein:said uncharged amino acids, positively charged amino acids, ornegatively charged amino acids are independently selected from the groupconsisting of S, T, Y, K, R, H, N, Q, D, and E; and/or said hydrophobicor hydrophilic amino acids are independently selected from the groupconsisting of using L, I, V, W, and F. 9: The antimicrobial peptide ofclaim 1, wherein said peptide further comprises a free amine at thecarboxyl terminus. 10: The antimicrobial peptide of claim 9, whereinsaid peptide comprises a free amine at the carboxyl terminus that isprovided by arginine or lysine. 11: The antimicrobial peptide of claim9, wherein said peptide comprises a free amine at the carboxyl terminusthat is provided by an amidated non-cationic residue. 12: Theantimicrobial peptide of claim 1, wherein said peptide is pegylated. 13:The antimicrobial peptide of claim 1, wherein said peptide bears one ormore protecting groups. 14: The antimicrobial peptide of claim 1,wherein said peptide bears one or more protecting groups selected fromthe group consisting of acetyl, amide, and 3 to 20 carbon alkyl groups,Fmoc, Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group,9-florenecarboxylic group, 9-fluorenone-1-carboxylic group,benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt),4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr),Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl(Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pmc), 4-methylbenzyl(MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl),Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys),1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl(2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z),2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom),t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum),t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).15: The antimicrobial peptide of claim 1, wherein said peptide comprisesall naturally occurring amino acids. 16: The antimicrobial peptide ofclaim 1, wherein said peptide comprises one or more “D” amino acidsand/or one or more beta amino acids. 17: (canceled)
 18. Theantimicrobial peptide of claim 1, wherein said peptide has at least a +3net positive charge at physiological pH. 19: The antimicrobial peptideof claim 1, wherein: n is 1.1; and said peptide comprises the motifH¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶, where H⁶ is an independently selectedhydrophobic amino acid. 20: The antimicrobial peptide of claim 19,wherein said peptide comprises an amino acid sequence selected from thegroup consisting of FKKFWKW FRRF (SEQ ID NO:31), LKRFLKWFKRF (SEQ IDNO:32) (B-34), KLFKRWKHLFR (SEQ ID NO:33) (B-35), RLLKRFKHLFK (SEQ IDNO:34) (B-36), FKTFLKWLHRF (SEQ ID NO:35) (B-37), IKQLLHFFQRF (SEQ IDNO:36) (B-38), KLLQTFKQIFR (SEQ ID NO:37) (B-39), RILKELKNLFK (SEQ IDNO:38) (B-40), LKQFVHFIHRF (SEQ ID NO:39) (B-41), VKTLLHIFQRF (SEQ IDNO:40) (B-42), KLVEQLKEIFR (SEQ ID NO:41) (B-43), RVLQEIKQILK (SEQ IDNO:42) (B-44), VKNLAELVHRF (SEQ ID NO:43) (B-45), ATHLLHALQRF (SEQ IDNO:44) (B-46), KLAENVKEILR (SEQ ID NO:45) (B-47), RALHEAKEALK (SEQ IDNO:46) (B-48), FHYFWHWFHRF (SEQ ID NO:47) (B-49), LYHFLHWFQRF (SEQ IDNO:48) (B-50), YLFQTWQHLFR (SEQ ID NO:49) (B-51), YLLTEFQHLFK (SEQ IDNO:50) (B-52), FKTFLQWLHRF (SEQ ID NO:51) (B-53), IKTLLHFFQRF (SEQ IDNO:52) (B-54), KLLQTFNQIFR (SEQ ID NO:53) (B-55), TILQSLKNIFK (SEQ IDNO:54) (B-56), LKQFVKFIHRF (SEQ ID NO:55) (B-57), VKQLLKIFNRF (SEQ IDNO:56) (B-58), KLVQQLKNIFR (SEQ ID NO:57) (B-59), RVLNQVKQILK (SEQ IDNO:58) (B-60), VKKLAKLVRRF (SEQ ID NO:59) (B-61), AKRLLKVLKRF (SEQ IDNO:60) (B-62), KLAQKVKRVLR (SEQ ID NO:61) (B-63), and RALKRIKHVLK (SEQID NO:62) (B-64). 21: The antimicrobial peptide of claim 20, whereinsaid peptide is amidated. 22: The antimicrobial peptide of claim 1,wherein: n is 1.4; and said peptide comprises the motifH¹C¹C²H²H³C³H⁴H⁵C⁴C⁵H⁶C⁶C⁷H⁷, where H⁶, and H⁷ are independentlyselected hydrophobic amino acids, and C⁶ and C⁷ are independentlyselected positively or negatively charged amino acids. 23: Theantimicrobial peptide of claim 22, wherein said peptide comprises anamino acid sequence selected from the group consisting of KLKKLLKKLKKLLK(SEQ ID NO:64) (α-5), LKLLKKLLKLLKKF (SEQ ID NO:65) (α-6),LQLLKQLLKLLKQF (SEQ ID NO:66) (α-7), RWRRWWRHFHHFFH (SEQ ID NO:68)(α-9), KLKKLLKRWRRWWR (SEQ ID NO:69) (α-10), RWRRLLKKLHHLLH (SEQ IDNO:70) (α-11), and KLKKLLKHLHHLLH (SEQ ID NO:71) (α-12). 24: Theantimicrobial peptide of claim 23, wherein said peptide is amidated. 25:The antimicrobial peptide of claim 1, wherein said peptide is labeledwith a detectable label.
 26. The antimicrobial peptide of claim 25,wherein said peptide is labeled with a detectable label selected fromthe group consisting of an enzymatic label, a fluorescent label, acolorimetric label, a spin label, and a radioactive label. 27: Theantimicrobial peptide of claim 1, wherein said peptide is attached to asecond antimicrobial peptide thereby forming a compound antimicrobialpeptide. 28: The antimicrobial peptide of claim 27, wherein saidcompound antimicrobial peptide is a fusion protein. 29: Theantimicrobial peptide of claim 27, wherein said second antimicrobialpeptide is: a peptide comprising the following amino acid motif or acircular permutation of the following amino acid motif:(H¹C¹C²H²H³C³H⁴H⁵C⁴C⁵)_(n) wherein: n ranges from 1 to 5 and canincrement by units of 0.1; H¹, H², H³, H⁴, and H⁵ are independentlyselected hydrophobic or hydrophilic amino acids; and C¹, C², C³, C⁴, andC⁵ are independently selected neutral amino acids, positively chargedamino acids, or negatively charged amino acids; or said peptidecomprising the seven contiguous amino acids wherein: all but two aminoacids are Arg or Trp, or derivatives or analogues thereof; the twonon-Arg or Trp amino acids are Lys or Phe, or derivatives or analoguesthereof; and the N-terminal residue is Arg or a derivative or analoguethereof. 30: The antimicrobial peptide of claim 27, wherein said secondantimicrobacterial peptide is a peptide listed in Table
 6. 31: Anantimicrobial peptide said peptide comprising seven contiguous aminoacids wherein: all but two amino acids are Arg or Trp, or derivatives oranalogues thereof; the two non-Arg or Trp amino acids are Lys or Phe, orderivatives or analogues thereof; and the N-terminal residue is Arg or aderivative or analogue thereof. 32: The antimicrobial peptide of claim31, wherein: all but two amino acids are Arg or Trp; the two non-Arg orTrp amino acids are Lys or Phe; and the N-terminal residue is Arg. 33:The antimicrobial peptide of claim 31, wherein said peptide comprises anamino acid sequence selected from the group consisting of RRRRWWW (SEQID NO:72) (1C-1), RRWWRRW (SEQ ID NO:73) (1C-2), RRRWWWR (SEQ ID NO:74)(IC-3), RWRWRWR (SEQ ID NO:75) (1C-4), RRRFWWR (SEQ ID NO:76) (2C-1),RRWWRRF (SEQ ID NO:77) (2C-2), RRRWWWF (SEQ ID NO:78) (2C-3), RWRWRWF(SEQ ID NO:79) (2C-4), RRRRWWK (SEQ ID NO:80) (3C-1), RRWWRRK (SEQ IDNO:81) (3C-2), RRRWWWK (SEQ ID NO:82) (3C-3), RWRWRWK (SEQ ID NO:83)(3C-4), RRRKWWK (SEQ ID NO:84) (4C-1), RRWKRRK (SEQ ID NO:85) (4C-2),RRRKWWK (SEQ ID NO:86) (4C-3), and RWRKRWK (SEQ ID NO:87) (4C-4). 34:The antimicrobial peptide of claim 31, wherein said peptide ispegylated. 35: The antimicrobial peptide of claim 31, wherein saidpeptide bears one or more protecting groups. 36: The antimicrobialpeptide of claim 31, wherein said peptide bears one or more protectinggroups selected from the group consisting of acetyl, amide, and 3 to 20carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group,1-fluorenecarboxylic group, 9-florenecarboxylic group,9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan),Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt),4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl(Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl (Tos), 2,2,5,7,8-pentamethylchroman-6-sulphonyl (Pmc), 4-methylbenzyl (MeBzl), 4-methoxybenzyl(MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz),3-nitro-2-pyridinesulphenyl (Npys),1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl(2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z),2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom),t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum),t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).37: The antimicrobial peptide of claim 31, wherein said peptidecomprises all naturally occurring amino acids. 38: The antimicrobialpeptide of claim 31, wherein said peptide comprises one or more “D”amino acids. 39: The antimicrobial peptide of claim 31, wherein saidpeptide comprises one or more beta amino acids. 40: The antimicrobialpeptide of claim 31, wherein said peptide is labeled with a detectablelabel. 41: The antimicrobial peptide of claim 40, wherein said peptideis labeled with a detectable label selected from the group consisting ofan enzymatic label, a fluorescent label, a colorimetric label, a spinlabel, and a radioactive label. 42: An acid-activated said peptidecomprising: an amphipathic helical peptide ranging in length from about7 to about 11 amino acids wherein the majority of charged residues areHis or a derivative or analogue thereof that caries a cationic charge atan acidic pH, wherein said peptide has substantially no antimicrobialactivity at neutral pH, but has antimicrobial activity against S. mutansat an acidic pH. 43: The antimicrobial peptide of claim 42, wherein allcharged residues are His or a derivative or analogue thereof that cariesa cationic charge at an acidic pH. 44: The antimicrobial peptide ofclaim 42, wherein said acidic pH is pH 6 or lower. 45: The antimicrobialpeptide of claim 42, wherein said peptide comprises alternating repeatsof HH and FF. 46: The antimicrobial peptide of claim 42 or 45, whereinsaid peptide comprises the amino acid sequence KLLK (SEQ ID NO:1) at oneor both termini. 47: The antimicrobial peptide of claim 42 or 45,wherein said peptide comprises the amino acid sequence KLLK (SEQ IDNO:1) at one or both termini wherein said KLLK is joined to the terminusby a linker. 48: The antimicrobial peptide of claim 27, wherein saidlinker is GAT (SEQ ID NO:2). 49: The antimicrobial peptide of claim 42,wherein said peptide comprises the amino acid sequence FHFFHHFFHFFHHF(SEQ ID NO:3). 50: The antimicrobial peptide of claim 42, wherein saidpeptide comprises an amino acid sequence selected from the groupconsisting of HHFFHHFHHFFHHF (SEQ ID NO:109) (AA-1), FHFFHHFFHFFHHF (SEQID NO:110) (AA-2), KLLKGATFHFFHHFFHFFHHF (SEQ ID NO:111) (AA-3),KLLKFHFFHHFFHFFHHF (SEQ ID NO:112) (AA-4), FHFFHHFFHFFHHFKLLK (SEQ IDNO:113) (AA-5), FHYFWHWFHRF (SEQ ID NO:114) (AA-6), and LYHFLHWFQRF (SEQID NO:115) (AA-7). 51: The antimicrobial peptide of claim 42, whereinsaid peptide bears one or more protecting groups. 52: The antimicrobialpeptide of claim 42, wherein said peptide bears one or more protectinggroups selected from the group consisting of acetyl, amide, and 3 to 20carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group,1-fluorenecarboxylic group, 9-florenecarboxylic group,9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan),Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt),4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl(Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl (Tos), 2,2,5,7,8-pentamethylchroman-6-sulphonyl (Pmc), 4-methylbenzyl (MeBzl), 4-methoxybenzyl(MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz),3-nitro-2-pyridinesulphenyl (Npys),1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl(2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z),2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom),t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum),t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).53: An antimicrobial peptide comprising a peptide selected from thegroup consisting of LKQKLKILF (SEQ ID NO:116 (S6L1-2), LKQLKAGIY (SEQ IDNO:117) (S6L1-3), VGKCVKLLY (SEQ ID NO:118) (S6L1-4), KFVKLI LAY (SEQ IDNO:119) (S6L1-5), KLVKLVFLY (SEQ ID NO:120) (S6L1-6), IKVFAKQKY (SEQ IDNO:121) (S6L1-7), and RFRHFQERY (SEQ ID NO:122) (S6L1-8). 54: Anantimicrobial peptide comprising a peptide selected from the groupconsisting of FVFRHKWVWKHRFLF (SEQ ID NO:123) (S3L8-1), VFI VWVHKHVLF(SEQ ID NO:124) (S3L8-2), WRWRARWRWRLRWRF (SEQ ID NO:125) (S3L8-3),WR1HLRARLHVKFRF (SEQ ID NO:126) (S3L8-4), LRIHARFKVHIRLKF (SEQ IDNO:127) (S3L8-5), FHIKFRVHLKVRFHF (SEQ ID NO:128) (S3L8-6),FHVK1HFRLHVKFHF (SEQ ID NO:129) (S3L8-7), LHIHAHFHVHIHLHF (SEQ IDNO:130) (S3L8-8), FKIHFRLKVHIRFKF (SEQ ID NO:131) (S3L8-9),FKAHIRFKLRVKFHF (SEQ ID NO:132) (S3L8-10), LKAKIKFKVKLKIKF (SEQ IDNO:133) (S3L8-11), WIWKHKFLHRHFLF (SEQ ID NO:134) (S3L8-12),VFLHRHVIKHKLVF (SEQ ID NO:135) (S3L8-13), FLHKHVLRHRIVF (SEQ ID NO:136)(S3L8-14), VFKHKIVHRHILF (SEQ ID NO:137) (S3L8-15), FLFKHLFLHRIFF (SEQID NO:138) (S3L8-16), LFKHILIHRVIF (SEQ ID NO:139) (S3L8-17),FLHKHLFKHKLF (SEQ ID NO:140) (S3L8-18), VFRHRFIHRHVF (SEQ ID NO:141)(S3L8-19), FIHKLVHKHVLF (SEQ ID NO:142) (S3L8-20), VLRHLFRHRIVF (SEQ IDNO:143) (S3L8-21), LVHKLILRHLLF (SEQ ID NO:144) (S3L8-22), VFKRVLI HKLIF(SEQ ID NO:145) (S3L8-23), IVRKFLFRHKVF (SEQ ID NO:146) (S3L8-24),VLKHVIAHKRLF (SEQ ID NO:147) (S3L8-25), FIRKFLFKHLF (SEQ ID NO:148)(S3L8-26), VIRHVWVRKLF (SEQ ID NO:149) (S3L8-27), FLFRHRFRHRLVF (SEQ IDNO:150) (S3L8-28), LFLHKHAKHKFLF (SEQ ID NO:151) (S3L8-29), FKHKFKHKFIF(SEQ ID NO:152) (S3L8-30), LRHRLRHRLIF (SEQ ID NO:153) (S3L8-31),LILKFLFKFVF (SEQ ID NO:154) (S3L8-32), VLIRILVRVIF (SEQ ID NO:155)(S3L8-33), FRHRFRHRF (SEQ ID NO:156) (S3L8-34), LKHKLKHKF (SEQ IDNO:157) (S3L8-35), FKFKHKLIF (SEQ ID NO:158) (S3L8-36), LRLRHRVLF (SEQID NO:159) (S3L8-37), FKFLFKFLF (SEQ ID NO:160) (S3L8-38), LRLFLRWLF(SEQ ID NO:161) (S3L8-39), FKFLFKHKF (SEQ ID NO:162) (S3L8-40),LRLFLRHRF (SEQ ID NO:163) (S3L8-41), FKFLFKF (SEQ ID NO:164) (S3L8-42),and LRLFLRF (SEQ ID NO:165) (S3L8-43). 55: A pharmaceutical formulationcomprising an antimicrobial peptide of claim 1; and pharmaceuticallyacceptable excipient. 56: The pharmaceutical formulation of claim 55,wherein said formulation is a unit dosage formulation. 57: Thepharmaceutical formulation of claim 55, wherein said excipient isacceptable for administration to an oral mucosa. 58: A home health careproduce comprising: an antimicrobial peptide according to claim 1,wherein said antimicrobial peptide is contained in a product selectedfrom the group consisting of toothpaste, mouthwash, a tooth whiteningstrip or solution, a contact lens storage, wetting, or cleaningsolution, dental floss, a toothpick, a toothbrush bristle, an oralspray, an oral lozenge, a nasal spray, an aerosolizer for oral and/ornasal application, and a wound dressing. 59: A method of inhibiting thegrowth and/or proliferation of a bacterium, said method comprisingcontacting said bacterium with a peptide according to claim 1, in anamount sufficient to inhibit growth and/or proliferation of saidbacterium. 60-66. (canceled) 67: A method of inhibiting the formation ofdental caries, said method comprising contacting teeth and or oralmucosa with a peptide according to claim 1 in an amount sufficient toinhibit growth and/or proliferation of S. mutans. 68: The method ofclaim 59, wherein contacting comprises contacting said teeth and/or oralmucosa with a composition selected from the group consisting of atoothpaste, a mouthwash, a whitening strip or solution, a lozenge, anaerosol, and a swab.